Method of treating a cancer

ABSTRACT

The present invention provides isolated nucleic acids encoding delta DNA methyltransferase 3B molecules that are involved in the treatment and prevention of cancers such as, but not limited to, lung cancer. The delta DNA methyltransferase 3B molecules of the present invention are found to play a critical role in promoter-specific methylation of tumor suppressor genes. The DNA methyltransferase 3B molecules of the present invention are provided as therapeutic targets for identifying inhibitors of DNA methyltransferase. Such inhibitors are contemplated for the treatment and/or prevention of cancers. In particular embodiments, the present invention involves the treatment and prevention of a non-small cell lung cancer.

The present invention claims priority to U.S. Provisional Patent Application Ser. No. 60/598,554, filed Aug. 3, 2004, which is incorporated by reference herein in its entirety.

BACKGROUND OF THE INVENTION

The government owns rights in the present invention pursuant to grant number DAMD17-01-1-01689-1 from the Department of Defense and grant numbers CA 68437 and CA 91844 from the National Cancer Institute.

FIELD OF THE INVENTION

The present invention relates generally to the fields of molecular biology, cancer biology and cancer therapy. More particularly, it concerns identification of therapeutic targets of DNA methyltransferase 3B molecules, such as, for example, delta DNA methyltransferase 3B variants, for treating a cancer including, but not limited to, lung cancer, and/or selecting a patient for treatment based on expression of the molecules.

DESCRIPTION OF RELATED ART

In the United States, lung cancer leads all other cancers in both incidence and mortality rate (Khuri et al., 2001). Lung cancer is the primary cause of cancer death among both men and women in the United States and worldwide.

Non-small cell lung cancer (NSCLC) constitutes 80% of all primary lung cancers, which are the leading cause of cancer-related death in both men and women in the United States (Greenlee et al., 2001). Despite advances in the treatment of the disease over the past two decades, the prognosis of patients with NSCLC has improved only modestly, with the 5-year overall survival rate increasing from 11% in the 1970s to 15% in the late 1990s (Greenlee et al., 2000). Patients with early-stage NSCLC generally have a better survival than those with advanced-stage tumors. For example, patients with stage I NSCLC are expected to have an approximate 60% 5-year overall survival rate after surgical resection of their primary tumors, while those with stage IIIA disease have an estimated 25% 5-year overall survival rate after surgery followed by radiation with or without chemotherapy.

Biological features of NSCLC are determined by underlying molecular alterations of the tumors, including inactivation of tumor suppressor genes (Niklinksi et al., 2001; Fong et al., 2003; Hirsch et al., 2001). Besides mutations and deletions of genes, it is now clear that de novo promoter hypermethylation is a common mechanism to inactivate tumor suppressor genes (Zochbauer-Muller et al., 2002; Foracs et al., 2001; Merlo et al., 1995). The p16^(INK4a) tumor suppressor gene located on 9p21 encodes a cyclin-dependent kinase inhibitor important for G1 cell cycle arrest (Zhang et al., 1999; Koh et al., 1995). Promoter hypermethylation of this gene has been frequently observed early in lung carcinogenesis, including in individuals exposed to tobacco carcinogens who do not exhibit evidence of cancer (Kim et al., 2001; Toyooka et al., 2001; Soria et al., 2002).

In contrast to p16^(INK4a), which is inactivated early in lung carcinogenesis (Soria et al., 2002; Belinsky et al., 1998), hypermethylation of another tumor suppressor gene, RASSF1A, occurs relatively late (Belinsky et al., 2002; Dammann et al., 2000; Pfeifer et al., 2002; Burbee et al., 2001), suggesting RASSF1A might be important in NSCLC progression. The RASSF1A tumor suppressor gene is located at 3p21, a region frequently deleted in NSCLC (Brauch et al. 1987). RASSF1A has been shown to bind to the Ras-GTP binding protein Norel, consistent with its role as a negative effector of Ras oncoprotein (Ortiz-Vegas et al., 2002).

It is that believed that DNA methytransferases play a critical role in the hypermethylation status of these tumor suppressor genes. Thus, DNA methyltransferases provide novel therapeutic targets in the treatment of cancers.

SUMMARY OF THE INVENTION

The present invention regards a new class of DNMT3B isoforms, referred to herein as deltaDNMT3Bs, ΔDNMT3Bs or DDNMT3Bs, that play an important role in tumorigenesis. The expression of these isoforms is initiated through a novel promoter, in specific embodiments. In particular aspects of the invention, the abnormal expression of the isoforms correlates with promoter methylation of tumor suppressor genes, thereby leading to at least partial inhibition of their expression. In other aspects, inactivation of the isoforms restores expression of a tumor suppressor gene, such as the exemplary RASSF1A gene, through demethylation of relevant hypermethylated promoters. In specific embodiments of the invention, the isoforms provide therapeutic targets of cancer that comprise inactivation of tumor suppressor genes, such as RASSF1A, through inactivation of promoter hypermethylation. Thus, the present invention provides a novel mechanism for providing cancer therapy separate from other methylation preventing agents by utilizing deltaDNMT3B in a novel promoter-specific demethylation.

In one aspect of the invention, deltaDNMT3B2/4 participates in regulation of RASSF1A promoter-specific methylation. The rapid demethylation of the promoter, activation of the gene expression, and prolonged inheritable effect of a single siRNA or antisense treatment, for example, provide significant implications in cancer therapy.

As described herein, at least seven transcription variants of DDNMT3B were identified as the result of alternative pre-mRNA processing. DDNMT3B variants but not DNMT3Bs were the predominant transcripts in both non-small cell lung cancer (NSCLC) cell lines and primary tumors. A striking association was observed between expression of DDNMT3B4, for example, and promoter methylation of RASSF1A, but a weaker association was observed with p16INK4A promoter methylation. A specific knockout of DDNMT3B4/2 by RNA interference or antisense approach results in a rapid and prolonged demethylation of RASSF1A promoter and reactivation of RASSF1A gene expression but not p16INK4A in NSCLC cell lines. Therefore, in specific aspects of the invention, DDNMT3Bs, such as DDNMT3B4/2, play an important role in maintenance of promoter-specific methylation of RASSF1A and shed light in understanding mechanisms of tissue-specific methylation. In specific embodiments, the isoform may bind directly to a promoter with specific DNA structure to prevent methylated cytosine from being demethylated or alternatively to prevent the structure from being repaired by DNA repair mechanisms. In further specific embodiments, the isoform interacts with specific chromotin structures of the promoters and forms complexes to protect the modified DNA structure.

Although in particular aspects the present invention provides methods and compositions of cancer therapy for cancers involving inactivation of tumor suppressor promoters through hypermethylation, such as the exemplary RASSF1A, the invention may be useful for any cancer, including lung cancer, brain cancer, prostate cancer, colon cancer, breast cancer, ovarian cancer, pancreatic cancer, liver cancer, spleen cancer, cervical cancer, melanoma, leukemia, head and neck cancer, esophageal cancer, thyroid cancer, testicular cancer, and so on. In a specific embodiment of the invention, the present invention is particularly useful for non-small cell lung cancer.

In an embodiment of the present invention, there is an isolated DNA methyltransferase-3B variant nucleic acid sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, or SEQ ID NO:14. In a specific embodiment, the nucleic acid sequence is comprised in an expression vector, for example, a viral or plasmid vector. The viral vector may be an adenoviral vector, an adeno-associated viral vector, a retroviral vector, a lentiviral vector, a herpes viral vector, polyoma viral vector or hepatitis B viral vector. The expression vector may be comprised in a non-viral delivery system. The non-viral delivery system may comprise one or more lipids. In a specific embodiment, the nucleic acid sequence is operatively linked to a promoter.

In an additional embodiment of the present invention, there is an isolated nucleic acid sequence encoding a DNA methyltransferase-3B variant having the amino acid sequence of SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, or SEQ ID NO:28.

In a further embodiment, there is a host cell comprising a nucleic acid sequence encoding a DNA methyltransferase-3B variant according to the present invention, wherein the nucleic acid sequence may be comprised in a vector.

In an additional embodiment of the present invention, there is an isolated DNA methyltransferase-3B variant having the amino acid sequence of SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, or SEQ ID NO:28.

In another embodiment of the present invention, there is a method of identifying an inhibitor of delta DNA methyltransferase 3B (dDNMT3B) activity, comprising: (a) providing in a cell or cell-free system a DNA methyltransferase 3B polypeptide corresponding to the sequence of SEQ. ID. NO:15, SEQ. ID. NO:16, SEQ. ID. NO:17, SEQ. ID. NO:18, SEQ. ID. NO:19, SEQ. ID. NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ. ID. NO:23, SEQ. ID. NO:24, SEQ. ID. NO:25, SEQ. ID. NO:26, SEQ. ID. NO:27, or SEQ ID NO:28; (b) contacting the DNA methyltransferase with a candidate substance (c) selecting an inhibitor of the DNA methyltransferase by assessing the effect of said candidate substance on DNA methyltransferase activity and (d) manufacturing the inhibitor.

In particular aspects of the invention, the candidate substance is a protein, a nucleic acid, a small molecule, an organo-pharmaceutical, or a combination thereof. The protein may be an antibody that binds immunologically to a dDNMT3B variant. The providing step may be further defined as providing a nucleic acid that encodes the DNA methyltransferase 3B polypeptide. In specific embodiments, the candidate substance is a nucleic acid, such as, for example, an antisense molecule or an siRNA molecule. In a particular embodiment, assessing comprises assaying for dDNMT3B activity, such as, for example, assessing the effect of the candidate substance on dDNMT3B activity comprises assaying for DNA methylation, which may be further defined as assaying for DNA methylation of a promoter. In a specific embodiment, the assessing step comprises polymerase chain reaction, a restriction endonuclease-based assay, or both.

In another embodiment of the present invention, there is a method of inhibiting the growth of a cancer cell comprising administering to the cell an effective amount of an inhibitor manufactured according to the present invention. In a specific embodiment, the administering of the inhibitor is further defined as inhibiting the enzymatic activity of DNA methyltransferase. The cell may be of any kind, but in specific embodiments the cancer cell is in a human. The cancer cell may be a cancer cell of the bladder, blood, bone, bone marrow, brain, breast, colon, esophagus, gastrointestine, gums, head, kidney, liver, lung, nasopharynx, neck, ovary, prostate, skin, stomach, testis, tongue, or uterus.

In particular embodiments, the cancer cell is a lung cancer cell, such as a malignant cancer cell or a metastatic lung cancer cell. In another specific embodiment, the lung cancer is a non-small cell lung cancer, a small cell lung cancer or a rare lung cancer cell. In another specific embodiment, the non-small cell lung cancer is a squamous cell carcinoma, an adenocarcinoma or a large cell carcinoma. The rare lung cancer cell may be an adenoid cystic carcinoma, a mesothelioma, a hamartoma, a lymphoma or a sarcoma. The lung cancer may be a carcinoid tumor. In a specific embodiment, the method further comprises inducing apoptosis in a cancer cell.

In another embodiment of the present invention, there is a nucleic acid sequence that is antisense to at least a portion of a DNA methyltransferase 3B nucleic acid of SEQ. ID. NO:1, SEQ. ID. NO:2, SEQ. ID. NO:3, SEQ. ID. NO:4, SEQ. ID. NO:5, SEQ. ID. NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, or SEQ ID NO:14. The nucleic acid sequence may be further defined as an siRNA sequence. The nucleic acid sequence may be further defined as being antisense to an exon/intron junction of a DNA methyltransferase 3B nucleic acid. In a specific embodiment, there is a DNA sequence encoding the antisense nucleic acid sequence.

In a specific embodiment, there is a pharmaceutical composition comprising a nucleic acid sequence of the present invention, in a pharmaceutically acceptable vehicle.

In an additional embodiment of the present invention, there is a method of inhibiting the growth of a cancer cell comprising providing to the cell an effective amount of a pharmaceutical composition in accordance with the present invention. In specific embodiments, the cancer cell is in a human cancer patient.

In specific aspects of the invention, there is selecting of a patient for treatment based on the expression of molecules of the invention. This is because in certain embodiments only tumors with abnormal expression of these molecules will respond to a therapy, such as an inhibitor, and therefore selection of patients based on the expression of the molecule is needed and may be considered part of treatment.

In certain aspects of the invention, small molecules are developed to target, for example exon-exon junctions and/or structures formed by these junctions to inhibitor the molecules.

Embodiments discussed with respect to one embodiment or example of the invention may be employed or implemented with respect to any other embodiment of the invention.

The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” Some embodiments of the invention may consist of or consist essentially of one or more elements, method steps, and/or methods of the invention. It is contemplated that any method or composition described herein can be implemented with respect to any other method or composition described herein.

Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

FIGS. 1A-1B. Examples of promoter methylation status measured using MSP. FIG. 1A—PCR products of methylated or unmethylated p16INK4a promoter from primary NSCLC and corresponding normal lung tissues. FIG. 1B—PCR products of methylated or unmethylated RASSF1A promoter from primary NSCLC and corresponding normal lung tissues. Molecular weight markers are listed on left side Neg indicates negative controls using unmethylated DNA Pos indicates positive controls using methylated DNA and methylation-specific primer sets Ts indicate primary tumors Ns indicate corresponding normal lung tissues; U indicates unmethylated promoter and M indicates methylated promoter.

FIGS. 2A-2F. Association between the p16INK4a promoter methylation status (FIGS. 2A, 2B, and 2C) or RASSF1A promoter methylation status (FIGS. 2D, 2E, and 2F) and overall, disease-specific, and disease-free survival. 0 indicates groups without methylation of promoter 1 indicates groups with methylation of promoter. E/N indicates number of events/total number in each group.

FIG. 3. Analysis of the effect of p16^(INK4a) and RASSF1A promoter methylation on patients' survival in patients with stage IIIA tumors.

FIG. 4. Association between the p16INK4a promoter methylation status (A, B, and C) or RASSF1A promoter methylation status (D, E, and F) and overall, disease-specific, and disease-free survival. - indicates groups without promoter methylation (number of events/total in group [E/N]: 12/28 for A 9/28 for B, 12/28 for C 6/17 for D 5/17 for E and 9/17 for F) ••• indicates groups with methylation of the p16INK4a or the RASSF1A promoter (E/N: 16/23 for A 13/23 for B 16/23 for C 14/21 for D 13/21 for E 14/21 for F) - - - indicates groups with methylation of both promoters (E/N: 13/19 for A 13/19 for B 14/19 for C 11/11 for D-F).

FIGS. 5A-5B. Expression of DNMT3B6. FIG. 5A—Expression of DNMT3B by RT-PCR using different 5′ primers located at exon 2 (E1), exon 4 (E3), and exon 6 (E5) of DNMT3B. FIG. 5B—Primer extension assay showing expression initiation sites of DNMT3B6.

FIGS. 6A-6B. Promoter activity of DNMT3B6 detected by luciferase assay. FIG. 6A—Schematic representation of reagents utilized in the assay. FIG. 6B—Effect of C/T transition polymorphism (C46359T) on the DNMT3B6 promoter activity. FIG. 6B—Effect of T-C transition polymorphism on promoter activity of DNMT3B6.

FIGS. 7A-7B. Identification of ΔDNMT3B variants highly expressed in lung cancer. FIG. 7A—Relative expression levels and pattern in NSCLC cell lines and paired primary lung cancers. FIG. 7B—Structural scheme of novel ΔDNMT3B isoforms.

FIGS. 8A-8D. Alternative or aberrant splicing variants of ΔDNMT3B subfamily. FIG. 8A—Location of the primers used to amplify individual ΔDNMT3B variants in this study. FIG. 8B—Expression patterns of ΔDNMT3B variants in NSCLC cell lines 1-7 represent ΔDNMT3B1-7, respectively. FIG. 8C—Expression patterns of DNMT3Bs, with more proximal exons corresponding to ΔDNMT3B1-4 and ΔDNMT3B6. FIG. 8D—Multiplex PCR using primer sets for DNMT3B1 and ΔDNMT3B1 with different ratios in concentration (concentration of DNMT3B1 primer set was serially diluted from 1-9 and serially increased from 1-9 1, DNMT3B1 primer set alone 9, ΔDNMT3B1 primer set alone 5, equal concentrations for both primer sets). The upper band represents the DNMT3B1 product and the lower band represents the ΔDNMT3B1 product. The lower panel shows relative intensity of the product bands.

FIGS. 9A-9E. Effects of ΔDNMT3B4/2 knockout on H1299 cells. FIG. 9A—Expression of ΔDNMT3B1, ΔDNMT3B2, and ΔDNMT3B4 at different time points after treatment measured by RT-PCR. FIG. 9B—Promoter methylation status of p16INK4a and RASSF1A at different time points after treatment measured by MSP. FIG. 9C—RASSF1A gene expression status at different time points after treatment measured by RT-PCR. For A, B, and C, M indicates size marker 1, treated with medium alone 2, treated with lipofectamine alone 3, treated with lipofectamine plus 40 nM GAPDH-specific siRNA 4, treated with lipofectamine plus 40 nM scramble siRNA 5, treated with lipofectamine plus 10 nM ΔDNMT3B4/2-specific siRNA 6, treated with 20 nM ΔDNMT3B4/2-specific siRNA 7, treated with 40 nM ΔDNMT3B4/2-specific siRNA 8, treated with 40 nM ΔDNMT3B4/2 antisense RNA −, negative control +, positive control. FIG. 9D—DNMT1 protein level in cells treated with or without ΔDNMT3B4/2-specific siRNA at the 48-h time point measured by Western blot analysis. The open circles indicate unmethylated cytosine residuals, and the solid circles indicate methylated cytosine residuals in the CpG sites. Each line represents DNA from a single clone. FIG. 9E—Methylation status of individual CpG sites in a RASSF1A promoter region from cells treated with or without ΔDNMT3B4/2-specific siRNA.

FIG. 10A-10B. Growth inhibition by siRNA to ΔDNMT3B4/2. FIG. 10A—Cell indexes (measured every 30 min) reflecting the cell number and the area of cell attachment to the plastic surface using ACEA RT-CES System. FIG. 10B—Cell cycle distribution measured by flow cytometry. (A) treated with medium (B) treated with lipofectamine alone (C) treated with lipofectamine plus 40 nM GAPDH-specific siRNA (D) Treated with lipofectamine plus 40 nM scramble siRNA (E) treated with lipofectamine plus 10 nM ΔDNMT3B4/2-specific siRNA; (F) treated with 20 nM ΔDNMT3B4/2-specific siRNA (G) treated with 40 nM ΔDNMT3B4/2-specific siRNA (H), treated with 40 nM ΔDNMT3B4/2 antisense RNA.

FIG. 11. Expression of Rare ΔDNMT3B5 (E), ΔDNMT3B6 (F), and ΔDNMT3B7 (G) and clinical outcome in NSCLC.

FIG. 12. Expresion of ΔDNMT3B4 in bronchial brush cell.

FIG. 13. Antibody recognition of ΔDNMT3B variant proteins in lysate of H460 NSCLC cell line.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

I. The Present Invention

The present invention overcomes the deficiencies of the current cancer therapies involving demethylating agents. Currently tested demethylating agents in cancer therapy are non-specific (therefore toxic), have low efficiency (only partial demethylation can be achieved), and are transient (DNA is methylated quickly after drug withdrawal), for example. Thus, studies to understand functions of individual DNA methyltransferases and variants thereof in the control of promoter specific methylation may lead to development of novel strategies for cancer therapy.

In specific aspects, the present invention relates to the identification of a novel DNA methyltransferase 3B (DNMT3B) subfamily, delta DNA methyltransferase 3B (ΔDNMT3B, DDNMT3B, or dDNMT3B), whose expression is initiated through a novel promoter. The present invention provides seven transcription variants of ΔDNMT3B that were identified as the result of alternative pre-mRNA processing.

The association between the promoter methylation status and tumorigenesis was examined, and it was determined that expression of ΔDNMT3B is a critical factor in promoter methylation of tumor suppressor genes, such as RASSF1A, in primary tumors. This indicates that inhibitors targeting delta DNA methyltransferase variants of the present invention may be useful to remove promoter demethylation, subsequently allowing expression of tumor suppressors.

The strong correlation between expression of a particular DNA methyltransferase variant and methylation of a specific gene promoter in primary tumors has never been reported previously. Knockout of an exemplary DDNMT3B variant resulted in demethylation of a specific promoter and activation of its gene expression, and this supports the critical role of the variant in control of the gene-specific promoter methylation. The complete demethylation of the promoter, such as in a 12 hour period, for example, indicates a novel, replication-independent mechanism regulating methylation in CpG sites, which provides information concerning gene-specific promoter methylation and replication-independent DNA demethylation.

The present invention provides at least nucleic acid and polypeptide or peptide compositions of the dDNMT3B subfamily and novel DNA methyltransferase 3B inhibitors, specifically delta DNA methyltransferase 3B (dDNMT3B) inhibitors, as therapeutic agents for treating or preventing cancers. Inhibition of DNMT3B may be of any suitable kind, including agents that inhibit at least partially one or more of the following: transcription, post-transcriptional process, translation, post-translational process, and/or protein activity and/or half-life, for example.

II. DNA Methyltransferase 3B (DNMT3B)

DNA methylation plays an essential role in normal development of a mammalian embryo by regulating gene transcription through genomic imprinting, X chromosome inactivation, and genomic stability (Jaenisch, 1997; Jones and Gonzalgo, 1997; Robertson and Wolfee, 2000, Surani, 1998). It is believed that DNA methylation patterns in somatic cells are established during gametogenesis and early embryonic development via consecutive waves of demethylation and de novo methylation (Monk et al., 1987).

DNMT3 consists of DNMT3A and DNMT3B and has been shown to be the major de novo DNA methyltransferases that preferentially methylate the cytosine in CpG sites (Okano et al., 1998; Li and Jaenisch, 2000). Human DNMT3B is highly homologous to the mouse gene and comprises 24 exons spanning about 47-kb of genomic DNA (GeneID: 1789 and 13436; GenBank Accession No. AL035071 (SEQ ID NO:64)). Two alternative 5′ exons of DNMT3B have been reported. However, both of these are believed to result in the same full-length DNMT3B protein (DNMT3B1 and DNMT3B2) (Robertson et al., 1999). Three additional transcriptional variants (DNMT3B3-6) resulting from alternative splicing have also been reported (Robertson et al., 1999). Some of the variants lacking the DNA methyltransferase activity compete with variants with the enzyme activity resulting in DNA hypomethylation (Saito et al., 2002), suggesting a complex role of the DNMT3B variants.

Increased expression of DNMT3B has been frequently observed in human cancer cell lines and primary tumors compared to most of the normal tissues except testis, pancreas, thyroid, and bone marrow (Robertson et al., 1999; Saito et al., 2002; Oue et al., 2001). Although the expression level of DNMT3B was found to be higher in cancer cell lines and primary tumor tissues, most of the studies did not find a strong association between the expression level of DNMT3B and promoter methylation status of tumor suppressor genes (Oue et al., 2001; Yakushiji et al., 2003; Sato et al., 2002), suggesting the presence of a more complex mechanism in regulating methylation of these promoters. In fact, only a small number of CpG-rich promoters are methylated in normal adult tissues or tumor tissues and these methylated promoters are different in different tissues, a phenomenon termed as “tissue-specific methylation” (Reik et al., 2001; Cedar, 1988). The methylation in CpG-rich promoter regions results in transcriptional silencing of corresponding genes, a major mechanism to inactivate tumor suppressor genes in tumorigenesis (Baylin et al., 2002).

Because the expression of DNMT3B might be highly regulated in the cell cycle, it was believed that the increased expression observed in tumors might be merely a reflection of an increased proliferation status (Robertson et al., 2000). Several recent studies further underscore this notion by demonstrating that the maintenance of methylated promoters of tumor suppressor genes could only be effectively disrupted when both DNMT3B and DNMT1 genes were knocked out while a single knockout of either DNMT3B or DNMT1 had minimal effects (Rhee et al., 2002; Rhee et al., 2000; Leu et al., 2003). However, these studies did not address potential effects of individual variants of DNMT3B. A dominant-negative effect of DNMT3b4, which lacks methyltransferase enzymatic motifs, in competing with DNMT3b3 has been suggested and resulted in DNA hypomethylation on pericentromeric satellite regions (Saito et al., 2002).

During tumorigenesis, de novo DNA methylation occurs in certain promoters, particularly tumor suppressor genes (Jones and Gonzalgo, 1997; Robertson and Wolffe, 2000). Global analysis of promoter methylation in different tumors indicates a number of promoters, including genes unlikely critical in tumorigenesis, are methylated. However, the patterns in terms of which genes and the total number of genes vary depending on the tumors (Esteller et al., 2003), suggesting that de novo promoter methylation occurring in tumorigenesis is a complex biologic operation. Weisenberger et al. (2004) recently studied several DNMT3B variants for their role in methylation of selected sequences and found that certain DNMT3B variants, despite the lack of a catalytically active domain, may still be biologically important in controlling methylation of certain sequence structures, although such variants alone may be not sufficient for the control.

The nucleic acid sequence of the seven exemplary ΔDNMT3B variants of the invention is provided respectively in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14. The corresponding encoded amino acid sequences for SEQ ID NOS:1-7 are provided respectively in SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, and SEQ ID NO:21. In specific embodiments, exemplary ΔDNMT3B variants lacking the C-terminal enzymatic domains are provided respectively in SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14. The corresponding encoded amino acid sequences for SEQ ID NOS:8-14 are provided respectively in SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, and SEQ ID NO:28.

III. Nucleic Acids Encoding DNA Methyltransferase 3B Molecules

In particular embodiments, the present invention provides isolated nucleic acid sequences encoding DNA methyltransferase 3B variants, and more particularly, delta DNA methyltransferase 3B (dDNMT3B) inhibitors such as antisense or siRNA molecules, for treating or preventing a cancer. In further particular embodiments, the present invention provides isolated nucleic acid sequences of DNA methyltransferase-3B variants comprising SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14, for example. The term “comprises SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14” means that the nucleic acid sequence substantially corresponds to a portion of SEQ ID NO:1 to SEQ ID NO:7. In some embodiments, the present invention employs a nucleic acid sequence that is antisense to at least a portion of the coding sequence of a DNA methyltransferase 3B polypeptide, and these nucleic acids correspond to the sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14.

The term “nucleic acid” generally refers to at least one molecule or strand of DNA, RNA or a derivative or mimic thereof, comprising at least one nucleotide base, such as, for example, a naturally occurring purine or pyrimidine base found in DNA (e.g., adenine “A,” guanine “G,” thymine “T,” and cytosine “C”) or RNA (e.g., A, G, uracil “U,” and C). The term “nucleic acid” encompasses the terms “oligonucleotide” and “polynucleotide.” These definitions generally refer to at least one single-stranded molecule, but in specific embodiments will also encompass at least one additional strand that is partially, substantially or fully complementary to the at least one single-stranded molecule. Thus, a nucleic acid may encompass at least one double-stranded molecule or at least one triple-stranded molecule that comprises one or more complementary strand(s) or “complement(s)” of a particular sequence comprising a strand of the molecule. An “isolated nucleic acid” as contemplated in the present invention may comprise transcribed nucleic acid(s), regulatory sequences, coding sequences, or the like, isolated substantially away from other such sequences, such as other naturally occurring nucleic acid molecules, regulatory sequences, polypeptide or peptide encoding sequences, etc.

Nucleic acids according to the present invention may comprise an entire DNA methyltransferase 3B polynucleotide, or any fragment or variant of DNA methyltransferase 3B as set forth herein. A nucleic acid of the present invention may be derived from genomic DNA, i.e., cloned directly from the genome of a particular organism. It is contemplated that the nucleic acids of the present invention may comprise complementary DNA (cDNA). The term “cDNA” is intended to refer to DNA prepared using messenger RNA (mRNA) as template. The advantage of using a cDNA, as opposed to genomic DNA or DNA polymerized from a genomic, non- or partially-processed RNA template, is that the cDNA primarily contains coding sequences of the corresponding protein. There may be times when the full or partial genomic sequence is preferred, such as where the non-coding regions are required for optimal expression or where non-coding regions such as introns are to be targeted in an antisense strategy.

It also is contemplated that a polynucleotide of a given DNA methyltransferase 3B variant may be represented by natural or synthetic variants that have slightly different nucleic acid sequences but, nonetheless, encode the same or homologous protein (Table 1). As used in this application, the term “polynucleotide” refers to a nucleic acid molecule that has been isolated free of total cellular nucleic acid. In exemplary embodiments, the invention concerns a nucleic acid sequence essentially as set forth in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:1, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14.

TABLE 1 Amino Acids Codons Alanine Ala A GCA GCC GCG GCU Cysteine Cys C UGC UGU Aspartic acid Asp D GAC GAU Glutamic acid Glu E GAA GAG Phenylalanine Phe F UUC UUU Glycine Gly G GGA GGC GGG GGU Histidine His H CAC CAU Isoleucine Ile I AUA AUC AUU Lysine Lys K AAA AAG Leucine Leu L UUA UUG CUA CUC CUG CUU Methionine Met M AUG Asparagine Asn N AAC AAU Proline Pro P CCA CCC CCG CCU Glutamine Gln Q CAA CAG Arginine Arg R AGA AGG CGA CGC CGG CGU Serine Ser S AGC AGU UCA UCC UCG UCU Threonine Thr T ACA ACC ACG ACU Valine Val V GUA GUC GUG GUU Tryptophan Trp W UGG Tyrosine Tyr Y UAC UAU

Allowing for the degeneracy of the genetic code, sequences that have at least about 80%, preferably at least about 90% and most preferably about 95% of nucleotides that are identical to the nucleotides of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14 are contemplated. Sequences that are essentially the same as those set forth in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14 may also be functionally defined as sequences that are capable of hybridizing to a nucleic acid sequence containing the complement of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14 under standard conditions. The term “functionally equivalent codon” is used herein to refer to codons that encode the same amino acid, such as the six codons for arginine or serine (Table 1), and also refers to codons that encode biologically equivalent amino acids, as discussed herein.

Naturally, the present invention also encompasses nucleic acid sequences that are complementary, or essentially complementary, to the sequences set forth herein, for example, in SEQ ID NO:1. Nucleic acid sequences that are “complementary” are those that are capable of base-pairing according to the standard Watson-Crick complementarity rules. As used herein, the terms “complementary sequences” and “essentially complementary sequences” means nucleic acid sequences that are substantially complementary to, as may be assessed by the same nucleotide comparison set forth above, or are able to hybridize to a nucleic acid segment of one or more sequences set forth herein, for example SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:1, SEQ ID NO:12, SEQ ID NO:13, and SEQ ID NO:14 under relatively stringent conditions such as those described herein. Such sequences may encode an entire DNA methyltransferase 3B molecule or functional or non-functional fragments thereof.

The hybridizing sequences may be short oligonucleotides. Sequences of 17 bases long should occur only once in the human genome and, therefore, suffice to specify a unique target sequence. Although shorter oligomers are easier to make and increase in vivo accessibility, numerous other factors are involved in determining the specificity of hybridization. Both binding affinity and sequence specificity of an oligonucleotide to its complementary target increases with increasing length. It is contemplated that exemplary oligonucleotides of about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80 or more base pairs will be used, although longer polynucleotides are contemplated. Such oligonucleotides will find use, for example, as probes in Southern and Northern blots and as primers in amplification reactions.

Suitable hybridization conditions will be well known to those of skill in the art. In certain applications, for example, substitution of amino acids by site-directed mutagenesis, it is appreciated that lower stringency conditions are required. Under these conditions, hybridization may occur even though the sequences of the probe and the target strand are not perfectly complementary, but are mismatched at one or more positions. Conditions may be rendered less stringent by increasing salt concentration and decreasing temperature. For example, a medium stringency condition could be provided by about 0.1 to 0.25 M NaCl at temperatures of about 37° C. to about 55° C., while a low stringency condition could be provided by about 0.15 M to about 0.9 M salt, at temperatures ranging from about 20° C. to about 55° C. Thus, hybridization conditions can be readily manipulated, and thus will generally be a method of choice depending on the desired results.

In other instances, hybridization may be achieved under conditions of, for example, 50 mM Tris-HCl (pH 8.3), 75 mm KCl, 3 mM MgCl₂, 10 mM dithiothreitol, at temperatures between approximately 20° C. to about 37° C. Other hybridization conditions utilized could include approximately 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 1.5 μM MgCl₂, at temperatures ranging from approximately 40° C. to about 72° C. Formamide and SDS also may be used to alter the hybridization conditions.

IV. Vectors Comprising Nucleic Acid Encoding DDNMT3B Molecules

Within certain embodiments of the present invention, an isolated nucleic acid sequence comprising a delta DNA methyltansferase 3B variant may be comprised in an expression vector. Expression requires that appropriate signals be provided in the vectors, which include various regulatory elements, such as enhancers/promoters from both viral and mammalian sources that drive expression of the genes of interest in host cells. Expression vectors utilized in the present invention may be a viral or plasmid vector.

The term “vector” is used to refer to a carrier nucleic acid molecule into which a nucleic acid sequence can be inserted for introduction into a cell where it can be replicated. A nucleic acid sequence can be “exogenous,” which means that it is foreign to the cell into which the vector is being introduced or that the sequence is homologous to a sequence in the cell but in a position within the host cell nucleic acid in which the sequence is ordinarily not found. Vectors include plasmids, cosmids, viruses (bacteriophage, animal viruses, etc.), and artificial chromosomes (e.g., YACs). One of skill in the art would be well equipped to construct a vector through standard recombinant techniques (see, for example, Maniatis et al., 1989 and Ausubel et al., 1994, both incorporated herein by reference).

The term “expression vector” refers to any type of genetic construct comprising a nucleic acid coding for a DNA methyltransferase molecule. In some cases, DNA molecules are then translated into a protein, polypeptide, or peptide. In other cases, these sequences are not translated, for example, in the production of antisense molecules or ribozymes. Expression vectors can contain a variety of “control sequences,” which refer to nucleic acid sequences necessary for the transcription and possibly translation of an operably linked coding sequence in a particular host cell. In addition to control sequences that govern transcription and translation, vectors and expression vectors may contain nucleic acid sequences that serve other functions as well and are described infra. It is contemplated in the present invention, that virtually any type of vector may be employed in any known or later discovered method to deliver nucleic acids encoding a DNA methyltransferase molecule. Where incorporation into an expression vector is desired, the nucleic acid encoding a DNA methyltransferase molecule may also comprise a natural intron or an intron derived from another gene. Such vectors may be viral or non-viral vectors as described herein, and as known to those skilled in the art. An expression vector comprising a nucleic acid encoding a DNA methyltransferase molecule may comprise a virus or engineered construct derived from a viral genome.

The ability of certain viruses to enter cells via receptor-mediated endocytosis and to integrate into the host cell genome and express viral genes stably and efficiently have made them attractive candidates for the transfer of foreign genes into mammalian cells (Ridgeway, 1988; Nicolas and Rubenstein, 1988; Baichwal and Sugden, 1986; Temin, 1986). The first viruses used as vectors were DNA viruses including the papovaviruses (simian virus 40, bovine papilloma virus, and polyoma) (Ridgeway, 1988; Baichwal and Sugden, 1986) adenoviruses (Ridgeway, 1988; Baichwal and Sugden, 1986) and adeno-associated viruses. Retroviruses also are attractive gene transfer vehicles (Nicolas and Rubenstein, 1988; Temin, 1986) as are vaccina virus (Ridgeway, 1988) and adeno-associated virus (Ridgeway, 1988). Such vectors may be used to (i) transform cell lines in vitro for the purpose of expressing the DNA methyltransferase molecules or inhibitors thereof, such as antisense or siRNA molecules of the present invention or (ii) to transform cells in vitro or in vivo to provide therapeutic molecules for gene therapy. Thus, the present invention contemplates viral vectors such as, but not limited to, an adenoviral vector, an adeno-associated viral vector, a retroviral vector, a lentiviral vector, a herpes viral vector, polyoma viral vector or hepatitis B viral vector.

In particular embodiments of the invention, a plasmid vector is contemplated for use to transform a host cell. In general, plasmid vectors containing replicon and control sequences that are derived from species compatible with the host cell are used in connection with these hosts. The vector ordinarily carries a replication site, as well as marking sequences that are capable of providing phenotypic selection in transformed cells. Plasmid vectors are well known and are commercially available. Such vectors include, but are not limited to, the commercially available pSupervector (OligoEngine, Seattle, Wash.) and pSilencer™ siRNA expression vectors (Ambion, Austin Tex.). Other vectors that may be employed in the present invention include, but are not limited to, the following eukaryotic vectors: pWLNEO, pSV2CAT, pOG44, PXT1, pSG (Stratagene) pSVK3, pBSK, pBR322, pUC vectors, vectors that contain markers that can be selected in mammalian cells, such as pcDNA3.1, episomally replicating vectors, such as the pREP series of vectors, pBPV, pMSG, pSVL (Pharmacia), adenovirus vector (AAV pCWRSV, Chatterjee et al. (1992)) retroviral vectors, such as the pBABE vector series, a retroviral vector derived from MoMuLV (pG1Na, Zhou et al., (1994)); and pTZ18U (BioRad, Hercules, Calif.).

Regulatory Elements. Throughout this application, the term “expression construct” is meant to include any type of genetic construct containing a nucleic acid coding for a DNA methyltransferase 3B molecule of the present invention in which part or all of the nucleic acid encoding sequence is capable of being transcribed. The transcript may be translated into a protein, but it need not be. Expression includes both transcription of a gene and translation of mRNA into a gene product. In other instances, expression only includes transcription of the nucleic acid encoding a gene of interest.

In preferred embodiments, the nucleic acid encoding a delta DNA methyltansferase is under transcriptional control of a promoter. A “promoter” refers to a DNA sequence recognized by the synthetic machinery of the cell, or introduced synthetic machinery, required to initiate the specific transcription of a gene. The phrases “operatively positioned,” “operatively linked,” “under control,” and “under transcriptional control” means that the promoter is in the correct location and orientation in relation to the nucleic acid to control transcriptional initiation and/or expression of that sequence.

The term promoter will be used here to refer to a group of transcriptional control modules that are clustered around the initiation site for RNA polymerase II. Much of the thinking about how promoters are organized derives from analyses of several viral promoters, including those for the HSV thymidine kinase (tk) and SV40 early transcription units. These studies, augmented by more recent work, have shown that promoters are composed of discrete functional modules, each consisting of approximately 7-20 bp of DNA, and containing one or more recognition sites for transcriptional activator or repressor proteins.

At least one module in each promoter functions to position the start site for RNA synthesis. The best-known example of this is the TATA box, but in some promoters lacking a TATA box, such as the promoter for the mammalian terminal deoxynucleotidyl transferase gene and the promoter for the SV40 late genes, a discrete element overlying the start site itself helps to fix the place of initiation.

Additional promoter elements regulate the frequency of transcriptional initiation. Typically, these are located in the region 30-110 bp upstream of the start site, although a number of promoters have recently been shown to contain functional elements downstream of the start site as well. The spacing between promoter elements frequently is flexible, so that promoter function is preserved when elements are inverted or moved relative to one another. In the tk promoter, the spacing between promoter elements can be increased to 50 bp apart before activity begins to decline. Depending on the promoter, it appears that individual elements can function either co-operatively or independently to activate transcription.

Promoters such as the human cytomegalovirus (CMV) immediate early gene promoter, the SV40 early promoter, the Rous sarcoma virus long terminal repeat, rat insulin promoter and glyceraldehyde-3-phosphate dehydrogenase can be used to obtain high-level expression of the coding sequence of interest. The use of other viral or mammalian cellular or bacterial phage promoters which are well-known in the art to achieve expression of a coding sequence of interest is contemplated as well, provided that the levels of expression are sufficient for a given purpose.

Enhancers are genetic elements that increase transcription from a promoter located at a distant position on the same molecule of DNA. Enhancers are organized much like promoters. That is, they are composed of many individual elements, each of which binds to one or more transcriptional proteins. The basic distinction between enhancers and promoters is operational. An enhancer region as a whole must be able to stimulate transcription at a distance; this need not be true of a promoter region or its component elements. On the other hand, a promoter must have one or more elements that direct initiation of RNA synthesis at a particular site and in a particular orientation, whereas enhancers lack these specificities. Promoters and enhancers are often overlapping and contiguous, often seeming to have a very similar modular organization.

Where a cDNA insert is employed, one will typically desire to include a polyadenylation signal to effect proper polyadenylation of the gene transcript. The nature of the polyadenylation signal is not believed to be crucial to the successful practice of the invention, and any such sequence may be employed such as human growth hormone and SV40 polyadenylation signals. Also contemplated as an element of the expression cassette is a terminator. These elements can serve to enhance message levels and to minimize read through from the cassette into other sequences.

Selectable Markers. In certain embodiments of the invention, cells containing a nucleic acid constructs of the present invention may be identified in vitro or in vivo by including a marker in the expression construct. Such markers would confer an identifiable change to the cell permitting easy identification of cells containing the expression construct. Usually the inclusion of a drug selection marker aids in cloning and in the selection of transformants, for example, genes that confer resistance to neomycin, puromycin, hygromycin, DHFR, GPT, zeocin and histidinol are useful selectable markers. Alternatively, enzymes such as herpes simplex virus thymidine kinase (tk) or chloramphenicol acetyltransferase (CAT) may be employed. Immunologic markers also can be employed. The selectable marker employed is not believed to be important, so long as it is capable of being expressed simultaneously with the nucleic acid encoding a gene product. Further examples of selectable markers are well known to one of skill in the art.

Multigene Constructs and IRES. In certain embodiments of the invention, the use of internal ribosome binding sites (IRES) elements are used to create multigene, or polycistronic, messages. IRES elements are able to bypass the ribosome scanning model of 5′ methylated Cap dependent translation and begin translation at internal sites (Pelletier and Sonenberg, 1988). IRES elements from two members of the picanovirus family (polio and encephalomyocarditis) have been described (Pelletier and Sonenberg, 1988), as well an IRES from a mammalian message (Macejak and Sarnow, 1991). IRES elements can be linked to heterologous open reading frames. Multiple open reading frames can be transcribed together, each separated by an IRES, creating polycistronic messages. By virtue of the IRES element, each open reading frame is accessible to ribosomes for efficient translation. Multiple genes can be efficiently expressed using a single promoter/enhancer to transcribe a single message.

Any heterologous open reading frame can be linked to IRES elements. This includes genes for secreted proteins, multi-subunit proteins, encoded by independent genes, intracellular or membrane-bound proteins and selectable markers. In this way, expression of several proteins can be simultaneously engineered into a cell with a single construct and a single selectable marker.

Host Cells. As used herein, the terms “cell,” “cell line,” and “cell culture” may be used interchangeably. All of these terms also include their progeny, which is any and all subsequent generations formed by cell division. It is understood that all progeny may not be identical due to deliberate or inadvertent mutations. A host cell may be “transfected” or “transformed,” which refers to a process by which exogenous nucleic acid is transferred or introduced into the host cell. A transformed cell includes the primary subject cell and its progeny. As used herein, the terms “engineered” and “recombinant” cells or host cells are intended to refer to a cell into which an exogenous nucleic acid sequence, such as, for example, a DNA methyltransferase 3B molecule or antisense or siRNA or a construct thereof. Therefore, recombinant cells are distinguishable from naturally occurring cells that do not contain a recombinantly introduced nucleic acid.

In certain embodiments, it is contemplated that nucleic acid or proteinaceous sequences may be co-expressed with other selected nucleic acid or proteinaceous sequences in the same host cell. Co-expression may be achieved by co-transfecting the host cell with two or more distinct recombinant vectors. Alternatively, a single recombinant vector may be constructed to include multiple distinct coding regions for nucleic acids, which could then be expressed in host cells transfected with the single vector.

V. Methods for Identifying Inhibitors DNA Methyltransferase 3B Activity

A. Inhibitors of Delta DNA Methyltransferase 3B

The present invention further comprises methods for identifying, making, generating, providing, manufacturing or obtaining inhibitors of delta DNA methyltransferase 3B activity. Delta DNA methyltransferase 3B nucleic acid or polypeptide may be used as a target in identifying compounds that inhibit, decrease or down-regulate its expression or activity in cancer cells, such as lung cancer cells. In other embodiments, compounds screened for would demethylate a hypermethylated promoter, such as a tumor suppressor gene promoter in a cancer cell. These assays may comprise random screening of large libraries of candidate substances; alternatively, the assays may be used to focus on particular classes of compounds selected with an eye towards structural attributes that are believed to make them more likely to inhibit the function of delta DNA methyltransferase 3B molecules. By function, it is meant that one may assay for inhibition of activity of delta DNA methyltransferase 3B in cancer cells, for demethylation of a methylated promoter or inhibition of the ability of the delta DNA methyltransferase 3B to methylate a promoter, and/or for the ability to increase apoptosism, for example.

To identify, make, generate, provide, manufacture or obtain a delta DNA methyltransferase 3B inhibitor, one generally will determine the activity of the delta DNA methyltransferase 3B molecule in the presence, absence, or both of the candidate substance, wherein an inhibitor is defined as any substance that down-regulates, reduces, inhibits or decreases delta DNA methyltransferase 3B expression or activity. For example, a method may generally comprise:

a) providing in a cell or cell free-system a DNA methyltransferase 3B polypeptide corresponding to the sequence of SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20 or SEQ ID NO:21;

b) contacting the DNA methyltransferase with a candidate substance; and

c) selecting an inhibitor of the DNA methyltransferase by assessing the effect of the candidate substance on DNA methyltransferase 3B activity. Upon identification of the inhibitor, the method may further provide manufacturing of the inhibitor.

Assays may be employed to assess the effect of the candidate substance on DNA methyltransferase activity, such as the following exemplary assays: (1) methylation specific PCR (MSP) or bisulfide sequencing analysis may be used to determine methylation status of specific promoters (2) RT-PCR may be used to determine reactivation of gene expression as a result of promoter demethylation of specific genes (3) global gene expression status measured by using DNA microarrays can be used to determine promoter methylation/demethylation status following manipulation of individual DNA methyltransferases; and/or (4) vectors containing specific promoter sequences with or without methylation may be co-transfected with vectors carrying individual DNA methyltransferase sequence into cells to determine at least one in vivo role of each isoform in controlling promoter methylation.

DNA methylation is a major determinant in the epigenetic silencing of genes. It is a complex process wherein three DNA methyltransferases catalyze the addition of a methyl group from S-adenosyl-L-methionine to the 5-carbon position of cytosine. A number of methods known to one of ordinary skill in the art may be used to detect DNA methylation. For example, such methods may include an enzyme based methodology or by chemical modificaton. In particular, such assays may include restriction endonuclease-based assays, restriction-enzyme based techniques, or developing methods based on polymerase chain reaction of sodium bisulfite-modified DNA, but is not limited to such. DNA array based techniques such as a differential methylation hybridization (Huang et al., 1999) assay may also be employed to perform a screen for hypermethylated promoter in a variety of cancer cell samples. PCR based methodologies may include methylation-sensitive restriction fingerprinting (Huang et al., 1997) to screen for changes in DNA methylation in tumors.

1. Inhibitors

As used herein the term “candidate substance” or “candidate compound” refers to any molecule that may potentially inhibit the activity of a delta DNA methyltransferase 3B molecule, that negatively affects its expression, or both. A delta DNA methyltransferase 3B inhibitor may be a compound that overall affects delta DNA methyltransferase 3B activity, which may be accomplished by inhibiting delta DNA methyltransferase 3B expression, function, or more directly by preventing its activity. Any compound or molecule described in the methods and compositions herein may be an inhibitor of delta DNA methyltransferase 3B activity.

The candidate substance may be a protein or fragment thereof, a small molecule, or even a nucleic acid molecule. It may prove to be the case that the most useful pharmacological compounds will be compounds that are structurally related to delta DNA methyltransferase 3B or other DNA methyltransferases, or that binds delta DNA methyltransferase 3B. In specific embodiments, the inhibitors may be dominant negative forms of the known DNMT3B forms or of the inventive DDNMT3B variants. Using lead compounds to help develop improved compounds is known as “rational drug design” and includes not only comparisons with known inhibitors, but predictions relating to the structure of target molecules.

Candidate compounds or inhibitors of the present invention will likely function to inhibit, decrease or down-regulate the expression or activity of delta DNA methyltransferase 3B in a cancer cell such as a lung cancer cell. Such candidate compounds may be inhibitors or regulators of DNA methyltransferases may have the ability to demethylate a methylated promoter or may likely be involved in controlling cellular proliferation in a cancer or tumor cell, such as lung cancer cells. These candidate compounds may be antisense molecules, ribozymes, interfering RNAs or siRNAs, antibodies (including single chain antibodies), small molecules, and/or organopharmaceuticals, but are not limited to such.

2. Rational Drug Design

The present invention also provides methods for developing drugs that inhibit delta DNA methyltransferase 3B activity that may be used to treat a cancer, such as lung cancer. One such method involves the prediction of the three dimensional structure of a validated DNA methyltransferase target using molecular modeling and computer stimulations. The resulting structure may then be used in docking studies to identify potential small molecule inhibitors. Inhibitors identified may then be tested in biochemical assays to further identify delta DNA methyltransferase 3B drug targets for cancer treatment, e.g., lung cancer treatment.

Rational drug design is therefore used to produce structural analogs of substrates for delta DNA methyltransferase 3B. By creating such analogs, it is possible to fashion drugs which are more active or stable than the natural molecules, which have different susceptibility to alteration or which may affect the function of various other molecules. In one approach, one would generate a three-dimensional structure for the delta DNA methyltransferase 3B targets of the invention or a fragment thereof. This could be accomplished by X-ray crystallography, computer modeling or by a combination of both approaches.

It is also possible to use antibodies to ascertain the structure of a target compound inhibitor. In principle, this approach yields a pharmacore upon which subsequent drug design can be based. It is possible to bypass protein crystallography altogether by generating anti-idiotypic antibodies to a functional, pharmacologically active antibody. As a mirror image of a mirror image, the binding site of anti-idiotype would be expected to be an analog of the original antigen. The anti-idiotype could then be used to identify and isolate peptides from banks of chemically- or biologically-produced peptides. Selected peptides would then serve as the pharmacore. Anti-idiotypes may be generated using the methods described herein for producing antibodies, using an antibody as the antigen.

On the other hand, one may simply acquire, from various commercial sources, small molecule libraries that are believed to meet the basic criteria for useful drugs in an effort to “brute force” the identification of useful compounds. Such libraries, including combinatorially generated libraries (e.g., peptide libraries), provide a rapid and efficient way to screen a large number of related (and unrelated) compounds for activity. Combinatorial approaches also lend themselves to rapid evolution of potential drugs by the creation of second, third and fourth generation compounds model of active, but otherwise undesirable compounds.

Candidate compounds may include fragments or parts of naturally-occurring compounds, or may be found as active combinations of known compounds, which are otherwise inactive. It is proposed that compounds isolated from natural sources, such as animals, bacteria, fungi, plant sources, including leaves and bark, and marine samples may be assayed as candidates for the presence of potentially useful pharmaceutical agents. It will be understood that the pharmaceutical agents to be screened could also be derived or synthesized from chemical compositions or man-made compounds. Thus, it is understood that the candidate substance identified by the present invention may be a peptide, polypeptide, polynucleotide, small molecule inhibitors or any other compounds that may be designed through rational drug design starting from known inhibitors or stimulators.

Other suitable compounds include antisense molecules, ribozymes, and antibodies (including single chain antibodies), each of which would be specific for the target molecule. Such compounds are described in greater detail elsewhere in this document. For example, an antisense molecule that bound to a translational or transcriptional start site, or splice junctions, would be ideal candidate inhibitors.

In addition, it is also contemplate that sterically similar compounds may be formulated to mimic the key portions of the structure of the inhibitors. Such compounds, may include peptidomimetics of peptide inhibitors. Regardless of the type of inhibitor identified by the present screening methods, the effect of the inhibition by such a compound results in the regulation of delta DNA methyltransferase 3B activity as compared to that observed in the absence of the added candidate substance.

The term “drug” as contemplated herein is intended to refer to a chemical entity, whether in the solid, liquid, or gaseous phase which is capable of providing a desired therapeutic effect when administered to a subject. The term “drug” should be read to include synthetic compounds, natural products and macromolecular entities such as polypeptides, polynucleotides, or lipids and also small entities such as neurotransmitters, ligands, hormones or elemental compounds. The term “drug” is meant to refer to that compound whether it is in a crude mixture or purified and isolated.

3. In Vitro Assays

A quick, inexpensive and easy assay to run is an in vitro assay. Such assays generally use isolated molecules, and can be run quickly and in large numbers, thereby increasing the amount of information obtainable in a short period of time. A variety of vessels may be used to run the assays, including test tubes, plates, dishes and other surfaces such as dipsticks or beads.

One example of a cell-free assay is a binding assay. While not directly addressing function, the ability of a compound to bind or contact to a target molecule, such as DNA methyltransferase of the present invention, in a specific fashion is strong evidence of a related biological effect, which can be assessed in a screening assay. For example, binding of a molecule to a delta DNA methyltransferase 3B molecule of the present invention may, in and of itself, be inhibitory, due to steric, allosteric or charge-charge interactions. The delta DNA methyltransferase 3B molecule may be either free in solution, fixed to a support, and/or expressed in or on the surface of a cell. Either the delta DNA methyltransferase 3B molecule or the compound may be labeled, thereby permitting measuring of the binding. Competitive binding formats can be performed in which one of the agents is labeled, and one may measure the amount of free label versus bound label to determine the effect on binding.

A technique for high throughput screening of compounds is described in WO 84/03564. Large numbers of small peptide test compounds are synthesized on a solid substrate, such as plastic pins or some other surface. Bound polypeptide is detected by various methods.

4. In Cyto Assays

The present invention also contemplates identifying compounds for their ability to inhibit a delta DNA methyltransferase 3B variant disclosed herein, in cells. Various cell lines can be utilized for such screening assays, including cells specifically engineered for this purpose. The present invention particularly contemplates the use of cancer cells, such as lung cancer cells. Depending on the assay, culture may be required. The cell is examined using any of a number of different physiologic assays. Alternatively, molecular analysis may be performed, for example, looking at protein expression, mRNA expression (including differential display of whole cell or polyA RNA) by methods as described herein and that are well known to those of skill in the art.

5. In Vivo Assays

In vivo assays involve the use of various animal models, including transgenic animals that have been engineered to have specific defects such as overexpression of a delta DNA methyltransferase 3B molecule, or that carry markers that can be used to measure the ability of a candidate substance to reach and effect different cells within the organism. Due to their size, ease of handling, and information on their physiology and genetic make-up, mice are a preferred embodiment, especially for transgenics. However, other animals are suitable as well, including rats, rabbits, hamsters, guinea pigs, gerbils, woodchucks, cats, dogs, sheep, goats, pigs, cows, horses and monkeys (including chimps, gibbons and baboons). Assays for inhibitors may be conducted using an animal model derived from any of these species.

In such assays, one or more candidate substances are administered to an animal, and the ability of the candidate substance(s) to alter one or more characteristics, as compared to a similar animal not treated with the candidate substance(s), identifies an inhibitor. The characteristics may be any of those discussed above with regard to delta DNA methyltransferase 3B activity, or it may be broader in the sense of “treating” the condition present in the animal.

Treatment of these animals with test compounds will involve the administration of the compound, in an appropriate form, to the animal. Administration will be by any route that could be utilized for clinical or non-clinical purposes, including but not limited to oral, nasal, buccal, topical or by a nebulizer or atomizer. Alternatively, administration may be by intratracheal instillation, bronchial instillation, intradermal, subcutaneous, intramuscular, intraperitoneal or intravenous injection. Specifically contemplated routes are systemic intravenous injection, regional administration via blood or lymph supply, or directly to an affected site.

Determining the effectiveness of a compound in vivo may involve measuring toxicity and dose response which can be performed in animals in a more meaningful fashion than in in vitro or in cyto assays.

VI. DNA Methyltransferase Inhibitors for Cancer Therapy

The present invention embodies a method of treating cancer such as lung cancer, by the delivery of a delta DNA methyltransferase 3B inhibitor to a cancer cell. Such a cell may be located in a patient having a cancer. Examples of cancers contemplated for treatment include leukemia, ovarian cancer, breast cancer, lung cancer, colon cancer, liver cancer, prostate cancer, testicular cancer, stomach cancer, brain cancer, bladder cancer, head and neck cancer, melanoma, and any other cancer that may be treated by inhibiting or decreasing the enzymatic activity of delta DNA methyltransferase 3B. Such inhibitors may include antisense molecules, RNA interference or siRNA methodology, or ribozymes.

A. Antisense Methodology

As discussed above, the present invention may also employ an antisense molecule in inhibiting the activity of a DNA methyltransferase, such as delta DNA methyltransferase. Antisense methodology takes advantage of the fact that nucleic acids tend to pair with “complementary” sequences. By complementary, it is meant that the polynucleotides are those capable of base-pairing according to the standard Watson-Crick complementary rules. That is, the larger purines will base pair with the smaller pyrimidines to form combinations of guanine paired with cytosine (G:C) and adenine paired with either thymine (A:T) in the case of DNA, or adenine paired with uracil (A:U) in the case of RNA. Inclusion of less common bases such as inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine and others in hybridizing sequences does not interfere with pairing.

Targeting double-stranded (ds) DNA with polynucleotides leads to triple-helix formation targeting RNA leads to double-helix formation. Antisense polynucleotides, when introduced into a target cell, specifically bind to their target polynucleotide and interfere with transcription, RNA processing, transport, translation and/or stability. Antisense molecules, or DNA encoding such antisense molecules, may be employed to inhibit gene transcription or translation or both within a host cell, either in vitro or in vivo, such as within a host animal, including a human subject.

Antisense molecules may be designed to bind to the promoter and/or other control regions, exons, introns or even exon-intron boundaries of a gene. It is contemplated that the most effective antisense constructs will include regions complementary to intron/exon splice junctions. Thus, it is proposed that a preferred embodiment includes one or more antisense molecules with complementarity to regions within about 50 of an intron-exon splice junction. It has been observed that some exon sequences can be included in the construct without seriously affecting the target selectivity thereof. The amount of exonic material included will vary depending on the particular exon and intron sequences used. One can readily test whether too much exon DNA is included simply by testing the constructs in vitro to determine whether normal cellular function is affected or whether the expression of related genes having complementary sequences is affected.

As stated above, “complementary” or “antisense” means polynucleotide sequences that are substantially complementary over their entire length and have very few base mismatches. For example, sequences of fifteen bases in length may be termed complementary when they have complementary nucleotides at thirteen or fourteen positions. Naturally, sequences which are completely complementary will be sequences which are entirely complementary throughout their entire length and have no base mismatches. Other sequences with lower degrees of homology also are contemplated. For example, an antisense construct which has limited regions of high homology, but also contains a non-homologous region (e.g., ribozyme see below) could be designed. These molecules, though having less than 50% homology, would bind to target sequences under appropriate conditions. It may be advantageous to combine portions of genomic DNA with cDNA or synthetic sequences to generate specific constructs. For example, where an intron is desired in the ultimate construct, a genomic clone will need to be used. The cDNA or a synthesized polynucleotide may provide more convenient restriction sites for the remaining portion of the construct and, therefore, would be used for the rest of the sequence.

In particular aspects of the invention, siRNA compositions may target an exon-exon junctions, such as of particular variants, including the exemplary one comprising sense strand provided in SEQ ID NO:61 and the antisense strand provided in SEQ ID NO:62, which targets the exemplary sequence of SEQ ID NO:63.

B. RNA Interference (RNAi)

The present invention also contemplates the use of RNA interference in inhibiting, reducing or downregulating the activity of delta DNA methyltransferase 3B molecules of the present invention. RNA interference (also referred to as “RNA-mediated interference” or RNAi) is a mechanism by which gene expression can be reduced or eliminated. Double stranded RNA (dsRNA) has been observed to mediate the reduction, which is a multi-step process. dsRNA activates post-transcriptional gene expression surveillance mechanisms that appear to function to defend cells from virus infection and transposon activity (Fire et al., 1998; Grishok et al., 2000; Ketting et al., 1999; Lin and Avery, 1999; Montgomery et al., 1998; Sharp, 1999; Sharp and Zamore, 2000; Tabara et al., 1999; Hutvagner et al., 2001; Tuschl, 2001; Waterhouse et al., 2001; Zamore, 2001). Activation of these mechanisms target mature, dsRNA-complementary mRNA for destruction. Moreover, dsRNA has been shown to silence genes in a wide range of systems, including plants, protozoans, fungi, C. elegans, Trypanasoma and Drosophila (Grishok et al., 2000; Sharp, 1999; Sharp and Zamore 2000).

RNAi offers major experimental advantages for the study of gene function. These advantages include a very high specificity, ease of movement across cell membranes, and prolonged down-regulation of the targeted gene. RNAi may be used to identify genes that are essential for a particular biological pathway, identify disease-causing genes, study structure function relationships, and implement therapeutics and diagnostics. As with other types of gene inhibitory compounds, such as antisense and triplex forming oligonucleotides, tracking these potential drugs in vivo and in vitro is important for drug development, pharmacokinetics, biodistribution, macro and microimaging metabolism and for gaining a basic understanding of how these compounds behave and function.

In RNAi the dsRNA is typically directed to an exon, although some exceptions to this have been shown (see Plasterk and Ketting, 2000). Also, a homology threshold (probably about 80-85% over 200 bases) is required. Most tested sequences are 500 base pairs or greater, though sequences of 30 nucleotides or fewer evade the antiviral response in mammalian cells (Baglioni et al., 1983; Williams, 1997). The targeted mRNA is lost after RNAi. The effect of RNAi is non-stoichiometric, and thus incredibly potent. In fact, it has been estimated that only a few copies of dsRNA are required to knock down >95% of targeted gene expression in a cell (Fire et al., 1998).

Due to a potent antiviral response pathway in mammalian cells that induces global changes in gene expression when the cells are challenged with long (>30 nucleotides) dsRNA molecules, RNAi was used in non-mammalian cells. This limitation in the art was overcome by the discovery of a method to bypass the antiviral response and induce gene specific silencing in mammalian cells (Elbashir et al., 2001). Several nucleotide (nt) dsRNAs with 2 nt 3′ overhangs were transfected into mammalian cells without inducing the antiviral response. These small dsRNAs, referred to as small interfering RNAs (siRNAs) proved capable of inducing the specific suppression of target genes. In addition, it was demonstrated that siRNAs could reduce the expression of several endogenous genes in human cells. The use of siRNAs to modulate gene expression in mammalian cells has since been demonstrated (Caplen et al., 2001; Hutvagner et al., 2001).

Thus, small interfering RNA (siRNA), which are generally 12-15 or 21-23 nucleotides in length and which possess the ability to mediate RNA interference are also contemplated in the present invention. For example, such siRNA may be of at least 21 nucleotides. siRNAs of the present invention may be synthesized chemically or may be produced recombinantly. They may be subsequently isolated and/or purified.

When made in vitro, siRNA is formed from one or more strands of polymerized ribonucleotide. When formed of only one strand, it takes the form of a self-complementary hairpin-type or stem and loop structure that doubles back on itself to form a partial duplex. The self-duplexed portion of the RNA molecule may be referred to as the “stem” and the remaining, connecting single stranded portion referred to as the “loop” of the stem and loop structure. When made of two strands, they are substantially complementary. siRNAs of the present invention may be synthesized chemically or may be produced recombinantly. They may be subsequently isolated and/or purified. dsRNA for use as siRNA may also be enzymatically synthesized through the use of RNA dependent RNA polymerases such as Q beta replicase, Tobacco mosaic virus replicase, brome mosaic virus replicase, potato virus replicase, etc. Methods for synthesizing dsRNA are well-described (Fire et al., 1998). Briefly, sense and antisense RNA are synthesized from DNA templates using T7 polymerase (MEGAscript, Ambion). After the synthesis is complete, the DNA template is digested with DNaseI and RNA purified by phenol/chloroform extraction and isopropanol precipitation. RNA size, purity and integrity are assayed on denaturing agarose gels. Sense and antisense RNA are diluted in potassium citrate buffer and annealed at 80° C. for 3 min to form dsRNA. As with the construction of DNA template libraries, a procedure may be employed to aid this time intensive procedure. The sum of the individual dsRNA species is designated as a “dsRNA library.”

Reaction conditions for use of these RNA polymerases are well known in the art (U.S. Pat. RE 35,443, and U.S. Pat. No. 4,786,600, each incorporated herein by reference). The result of contacting the appropriate template with an appropriate polymerase is the synthesis of an RNA product, which is typically double-stranded. In some instances a single stranded RNA or single stranded DNA template may be utilized. If utilizing a single stranded DNA template, the enzymatic synthesis results in a hybrid RNA/DNA duplex that is also contemplated as useful as siRNA.

The templates for enzymatic synthesis of siRNA are nucleic acids, typically, though not exclusively DNA. A nucleic acid may be made by any technique known to one of ordinary skill in the art. Non-limiting examples of synthetic nucleic acid, particularly a synthetic oligonucleotide, include a nucleic acid made by in vitro chemical synthesis using phosphotriester, phosphite or phosphoramidite chemistry and solid phase techniques such as described in EP 266,032, incorporated herein by reference, or via deoxynucleoside H-phosphonate intermediates as described by Froehler et al. (1986), and U.S. Pat. No. 5,705,629, each incorporated herein by reference. A non-limiting example of enzymatically produced nucleic acid include one produced by enzymes in amplification reactions such as PCR™ (see for example, U.S. Pat. Nos. 4,683,202 and 4,682,195, each incorporated herein by reference), or the synthesis of oligonucleotides described in U.S. Pat. No. 5,645,897, incorporated herein by reference. A non-limiting example of a biologically produced nucleic acid includes recombinant nucleic acid production in living cells (see for example, Sambrook, 2001; incorporated herein by reference). Methods for the production of siRNA to induce gene silencing can be found in United States Patent Application 20030166282, incorporated herein by reference.

The nucleic acid(s) of the present invention, regardless of the length of the sequence itself, may be combined with other nucleic acid sequences, including but not limited to, promoters, enhancers, polyadenylation signals, restriction enzyme sites, multiple cloning sites, coding segments, and the like, to create one or more nucleic acid construct(s). The overall length may vary considerably between nucleic acid constructs. Thus, a nucleic acid segment of almost any length may be employed, with the total length preferably being limited by the ease of preparation or use in the intended protocol.

C. Ribozymes

The present invention also contemplates the use of DNA methyltransferase 3B specific ribozymes to down-regulate or inhibit delta DNA methyltransferase 3B enzymatic activity. Ribozymes are RNA-protein complexes that cleave nucleic acids in a site-specific fashion. Ribozymes comprise of eight classes including seven that modify the nucleic acid backbone which include hammerhead, hairpin, HDV (hepatitis delta virus), ribonuclease P, group I intron, group II intron, and VS ribozyme. The eighth type, the ribosome's peptidyl transferase center, builds peptide bonds.

Ribozymes have specific catalytic domains that possess endonuclease activity (Kim and Cook, 1987;; Gerlach et al., 1987; Forster and Symons, 1987). For example, a large number of ribozymes accelerate phosphoester transfer reactions with a high degree of specificity, often cleaving only one of several phosphoesters in an oligonucleotide substrate (Michel and Westhof, 1990; Reinhold-Hurek and Shub, 1992). This specificity has been attributed to the requirement that the substrate binds via specific base-pairing interactions to the internal guide sequence (“IGS”) of the ribozyme prior to chemical reaction.

Ribozyme catalysis has primarily been observed as part of sequence-specific cleavage/ligation reactions involving nucleic acids (Joyce, 1989). For example, U.S. Pat. No. 5,354,855 reports that certain ribozymes can act as endonucleases with a sequence specificity greater than that of known ribonucleases and approaching that of the DNA restriction enzymes. Thus, sequence-specific ribozyme-mediated inhibition of gene expression may be particularly suited to therapeutic applications (Scanlon et al., 1991; Sarver et al., 1990).

VII. Generating Antibodies Reactive with DNA Methyltransferase 3B Molecules

In a particular embodiment, the present invention contemplates antibodies that are immunoreactive with a DNA methyltransferase 3B or variants thereof. Such an antibody can be a polyclonal or a monoclonal antibody, although in a preferred embodiment the antibody is a monoclonal antibody. Means for preparing and characterizing antibodies are well known in the art (see, e.g., Harlow and Lane, 1988). Briefly, a polyclonal antibody is prepared by immunizing an animal with an immunogen comprising a polypeptide of the present invention and collecting antisera from that immunized animal. A wide range of animal species can be used for the production of antisera. Typically an animal used for production of anti-antisera is a non-human animal including rabbits, mice, rats, hamsters, pigs or horses. Because of the relatively large blood volume of rabbits, a rabbit is a preferred choice for production of polyclonal antibodies.

Antibodies, both polyclonal and monoclonal, specific for an antigen may be prepared using conventional immunization techniques, as are generally known to those of skill in the art. A composition containing antigenic epitopes of the compounds of the present invention can be used to immunize one or more experimental animals, such as a rabbit or mouse, which will then proceed to produce specific antibodies against the compounds of the present invention. Polyclonal antisera may be obtained, after allowing time for antibody generation, simply by bleeding the animal and preparing serum samples from the whole blood.

It is proposed that the antibodies of the present invention will find useful application in standard immunochemical procedures, such as ELISA and Western blot methods and in immunohistochemical procedures such as tissue staining, as well as in other procedures which may utilize antibodies specific to DNA methyltransferase 3B variants.

In general, both polyclonal and monoclonal antibodies against delta DNA methyltransferase 3B variants of the present invention may be used in a variety of embodiments. For example, they may be employed in antibody cloning protocols to obtain cDNAs or genes encoding other DNA methyltransferase 3B molecules. They may also be used in inhibition studies to analyze the effects of delta DNA methyltransferase 3B in cells or animals. Antibodies comprising DNA methyltransferase 3B variants will also be useful in immunolocalization studies to analyze the distribution of these molecules during various cellular events, for example, to determine the cellular or tissue-specific distribution of DNA methyltransferase 3B polypeptides at different points in the cell cycle. A particularly useful application of such antibodies is in purifying native or recombinant DNA methyltransferase 3B molecules, for example, using an antibody affinity column. The operation of such immunological techniques are well known to those of skill in the art.

As is well known in the art, a given composition may vary in its immunogenicity. It is often necessary therefore to boost the host immune system, as may be achieved by coupling a peptide or polypeptide immunogen to a carrier. Exemplary and preferred carriers are keyhole limpet hemocyanin (KLH) and bovine serum albumin (BSA). Other albumins such as ovalbumin, mouse serum albumin or rabbit serum albumin can also be used as carriers. Means for conjugating a polypeptide to a carrier protein are well known in the art and include glutaraldehyde, m-maleimidobencoyl-N-hydroxysuccinimide ester, carbodiimide and bis-biazotized benzidine.

It is also well known in the art, that the immunogenicity of a particular immunogen composition can be enhanced by the use of non-specific stimulators of the immune response, known as adjuvants. Exemplary and preferred adjuvants include complete Freund's adjuvant (a non-specific stimulator of the immune response containing killed Mycobacterium tuberculosis), incomplete Freund's adjuvants and aluminum hydroxide adjuvant.

The amount of immunogen composition used in the production of polyclonal antibodies varies upon the nature of the immunogen as well as the animal used for immunization. A variety of routes can be used to administer the immunogen (subcutaneous, intramuscular, intradermal, intravenous and intraperitoneal). The production of polyclonal antibodies may be monitored by sampling blood of the immunized animal at various points following immunization. A second, booster, injection may also be given. The process of boosting and titering is repeated until a suitable titer is achieved. When a desired level of immunogenicity is obtained, the immunized animal can be bled and the serum isolated and stored, and/or the animal can be used to generate mAbs.

MAbs may be readily prepared through use of well-known techniques, such as those exemplified in U.S. Pat. No. 4,196,265, incorporated herein by reference. Typically, this technique involves immunizing a suitable animal with a selected immunogen composition, e.g., a purified or partially purified protein, polypeptide or peptide or cell expressing high levels. The immunizing composition is administered in a manner effective to stimulate antibody producing cells. Rodents such as mice and rats are preferred animals, however, the use of rabbit, sheep or frog cells is also possible. The use of rats may provide certain advantages (Goding, 1986), but mice are preferred, with the BALB/c mouse being most preferred as this is most routinely used and generally gives a higher percentage of stable fusions.

VIII. Delivery of a DNMT3B Inhibitor to a Cell

In some embodiments of the present invention delivery of a nucleic acid encoding a DNA methyltransferase inhibitor such as an antisense or siRNA or an expression construct thereof to a cell is contemplated. Virtually any method by which nucleic acids can be introduced into a cell, or an organism may be employed with the current invention, as described herein or as would be known to one of ordinary skill in the art.

Such methods include, but are not limited to direct delivery of a nucleic acid by: injection (U.S. Pat. Nos. 5,994,624, 5,981,274, 5,945,100, 5,780,448, 5,736,524, 5,702,932, 5,656,610, 5,589,466 and 5,580,859, each incorporated herein by reference) microinjection (Harland and Weintraub, 1985; U.S. Pat. No. 5,789,215, incorporated herein by reference); electroporation (U.S. Pat. No. 5,384,253, incorporated herein by reference Tur-Kaspa et al., 1986; Potter et al., 1984) calcium phosphate precipitation (Graham and Van Der Eb, 1973; Chen and Okayama, 1987; Rippe et al., 1990) using DEAE-dextran followed by polyethylene glycol (Gopal, 1985) direct sonic loading (Fechheimer et al., 1987) liposome mediated transfection (Nicolau and Sene, 1982; Fraley et al., 1979; Nicolau et al., 1987; Wong et al., 1980; Kaneda et al., 1989; Kato et al., 1991) receptor-mediated transfection (Wu and Wu, 1987; Wu and Wu, 1988) microprojectile bombardment (PCT Application Nos. WO 94/09699 and 95/06128; U.S. Pat. Nos. 5,610,042 5,322,783 5,563,055, 5,550,318, 5,538,877 and 5,538,880, and each incorporated herein by reference) agitation with silicon carbide fibers (Kaeppler et al., 1990; U.S. Pat. Nos. 5,302,523 and 5,464,765, each incorporated herein by reference) PEG-mediated transformation of protoplasts (Omirulleh et al., 1993; U.S. Pat. Nos. 4,684,611 and 4,952,500, each incorporated herein by reference) desiccation/inhibition-mediated DNA uptake (Potrykus et al., 1985) or any combination of such methods.

In other embodiments, it is contemplated that a nucleic acid encoding an siRNA or an expression construct thereof may be delivered to a cell by hydrodynamic transfection/injection, or by liposomes.

It is also contemplated in the present invention that a siRNA may be delivered directly to a cell. In other embodiments, the siRNA may be delivered to a cell indirectly by introducing one or more vectors that encode both single strands of a siRNA (or, in the case of a self-complementary RNA, the single self-complementary strand) into the cell. The vectors of these embodiments contain elements of the templates described above such that the RNA is transcribed inside the cell, annealed to form siRNA and effects attenuation of the target gene expression. See WO 99/32619, WO 00/44914, WO 01/68836 (each of which is expressly incorporated herein by reference) and references therein for further examples of methods known in the art for introducing siRNA into cells. In some embodiments, an siRNA of the present invention may be delivered along with components that enhance RNA uptake by the cell, stabilize the annealed strands, or otherwise increase inhibition of DNA methyltransferase 3B activity.

Wherein the inhibitor is not a nucleic acid, such as an antibody, for example, standard means in the art may be utilized to deliver the inhibitor, such as by liposomes.

IX. Therapeutic/Pharmaceutical Compositions

In some embodiments, the present invention provides a method of treating or preventing a cancer by providing or administering to a patient a therapeutically effective amount of DNA methyltransferase 3B inhibitor, such as a delta DNA methytransferase 3B inhibitor which includes but is not limited to an antisense or siRNA molecule.

“Therapeutically effective amounts” are those amounts effective to produce beneficial results, particularly with respect to cancer treatment, in the recipient animal or patient. Such amounts may be initially determined by reviewing the published literature, by conducting in vitro tests or by conducting metabolic studies in healthy experimental animals. Before use in a clinical setting, it may be beneficial to conduct confirmatory studies in an animal model, preferably a widely accepted animal model of the particular disease to be treated. Preferred animal models for use in certain embodiments are rodent models, which are preferred because they are economical to use and, particularly, because the results gained are widely accepted as predictive of clinical value.

Diseases contemplated for treatment with the DNA methyltransferase 3B inhibitors of the present invention include, but are not limited to, cancers. Examples of cancers contemplated for treatment with a delta DNA methyltransferase 3B inhibitor may include breast cancer, lung cancer, head and neck cancer, bladder cancer, bone cancer, bone marrow cancer, brain cancer, colon cancer, esophageal cancer, gastrointestinal cancer, gum cancer, kidney cancer, liver cancer, nasopharynx cancer, ovarian cancer, prostate cancer, skin cancer, stomach cancer, testis cancer, tongue cancer, or uterine cancer. In some instances the cancer to be treated using a delta DNA methyltransferase 3B inhibitor as disclosed herein, may be a malignant or metastatic cancer but not limited to such.

To inhibit DNA methylation, kill cells, induce cell cycle arrest, inhibit cell growth, inhibit metastasis, inhibit angiogenesis or otherwise reverse or reduce the malignant phenotype of cancer cells, using the methods and compositions of the present invention, one would generally contact a cell with the DNA methyltransferase 3B inhibitor, in particular a delta DNA methyltransferase inhibitor. The terms “contacted” and “exposed,” when applied to a cell, tissue or organism, are used herein to describe the process by which the therapeutic compositions of the invention is delivered to a target cell, tissue or organism or are placed in direct juxtaposition with the target cell, tissue or organism. To achieve cell killing or stasis, an amount effective of the therapeutic composition is delivered to one or more cells to kill the cell(s) or prevent them from dividing.

Pharmaceutical aqueous compositions of the present invention comprise the delta DNA methyltransferase 3B inhibitor and/or an additional agent(s) dissolved or dispersed in a pharmaceutically acceptable carrier or aqueous medium. The phrases “pharmaceutically or pharmacologically acceptable” refers to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to a human. As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.

The actual dosage amount of a delta DNA methyltransferase 3B inhibitory composition of the present invention (and/or an additional agent) for administration to a patient can be determined by physical and physiological factors such as body weight, severity of condition, idiopathy of the patient and on the route of administration. With these considerations in mind, the dosage of a lipid composition for a particular subject and/or course of treatment can readily be determined.

Treatment may vary depending upon the host treated and the particular mode of administration. For example, in the invention the dose range of a DNA methyltransferase 3B inhibitor may be about 0.5 mg/kg body weight to about 500 mg/kg body weight. The term “body weight” is applicable when an animal is being treated. When isolated cells are being treated, “body weight” as used herein should read to mean “total cell weight”. The term “total weight may be used to apply to both isolated cell and animal treatment. All concentrations and treatment levels are expressed as “body weight” or simply “kg” in this application are also considered to cover the analogous “total cell weight” and “total weight” concentrations. However, those of skill will recognize the utility of a variety of dosage range, for example, 1 mg/kg body weight to 450 mg/kg body weight, 2 mg/kg body weight to 400 mg/kg body weight, 3 mg/kg body weight to 350 mg/kg body weight, 4 mg/kg body weight to 300 mg/kg body weight, 5 mg/kg body weight to 250 mg/kg body weighty, 6 mg/kg body weight to 200 mg/kg body weight, 7 mg/kg body weight to 150 mg/kg body weight, 8 mg/kg body weight to 100 mg/kg body weight, or 9 mg/kg body weight to 50 mg/kg body weight. Further, those of skill will recognize that a variety of different dosage levels will be of use, for example, 1 mg/kg, 2 mg/kg, 3 mg/kg, 4 mg/kg, 5 mg/kg, 7.5 mg/kg, 10 mg/kg, 12.5 mg/kg, 15 mg/kg, 17.5 mg/kg, 20 mg/kg, 25 mg/kg, 30 mg/kg, 35 mg/kg, 40 mg/kg, 45 mg/kg, 50 mg/kg, 60 mg/kg, 70 mg/kg, 80 mg/kg, 90 mg/kg, 100 mg/kg, 120 mg/kg, 140 mg/kg, 150 mg/kg, 160 mg/kg, 180 mg/kg, 200 mg/kg, 225 mg/kg, 250 mg/kg, 275 mg/kg, 300 mg/kg, 325 mg/kg, 350 mg/kg, 375 mg/kg, 400 mg/kg, 450 mg/kg, 500 mg/kg, 550 mg/kg, 600 mg/kg, 700 mg/kg, 750 mg/kg, 800 mg/kg, 900 mg/kg, 1000 mg/kg, 1250 mg/kg, 1500 mg/kg, 1750 mg/kg, 2000 mg/kg, 2500 mg/kg, and/or 3000 mg/kg. Of course, all of these dosages are exemplary, and any dosage in-between these points is also expected to be of use in the invention. Any of the above dosage ranges or dosage levels may be employed for a DNA methyltransferase 3B inhibitor of the present invention.

In certain embodiments, pharmaceutical compositions may comprise, for example, at least about 0.1% of an active compound. In other embodiments, the active compound may comprise between about 2% to about 75% of the weight of the unit, or between about 25% to about 60%, for example, and any range derivable therein. As is well known in the art, a specific dose level of active compounds such as a delta DNA methyltransferase inhibitor, for any particular patient depends upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, sex, diet, time of administration, route of administration, rate of excretion, drug combination, and the severity of the particular disease undergoing therapy. The person responsible for administration will determine the appropriate dose for the individual subject. Moreover, for human administration, preparations should meet sterility, pyrogenicity, and general safety and purity standards as required by FDA Office of Biologics standards.

A delta DNA methyltransferase 3B inhibitor as a therapeutic agent may be administered to a subject more that once and at intervals ranging from minutes to weeks. One would generally ensure that a significant period of time did not expire between the time of each delivery, such that the agent would still be able to exert an advantageous effect on the cell. In some situations, it may be desirable to extend the time period for treatment significantly, however, where several days (2, 3, 4, 5, 6 or 7) to several weeks (1, 2, 3, 4, 5, 6, 7 or 8) lapse between the respective administrations.

Administration of delta DNA methyltransferase 3B inhibitor to a patient may be by any method know in the art for delivery of a therapeutic agent to a patient. The inhibitors of the present invention can be administered intravenously, intradermally, intraarterially, intraperitoneally, intralesionally, intracranially, intraarticularly, intraprostaticaly, intrapleurally, intratracheally, intranasally, intravitreally, intravaginally, rectally, topically, intratumorally, intramuscularly, intraperitoneally, subcutaneously, intravesicularlly, mucosally, intrapericardially, orally, topically, locally and/or using aerosol, injection, infusion, continuous infusion, localized perfusion bathing target cells directly or via a catheter and/or lavage. For example, a delta DNA methyltransferase 3B inhibitory composition of the present invention may be formulated for parenteral administration, e.g., formulated for injection via the intravenous, intramuscular or sub-cutaneous routes, though other routes such aerosol administration may be used. The delta DNA methyltransferase 3B inhibitory compositions of the present invention may be formulated for non-pressures preparations, such as in a nebulizer or an atomizer. The preparation of an aqueous composition that contains the a delta DNA methyltransferase 3B inhibitory composition of the present invention and/or and additional agent as an active ingredient will be known to those of skill in the art in light of the present disclosure, as exemplified by Remington's Pharmaceutical Sciences, 16th Ed. Mack Publishing Company, 1980, incorporated herein by reference. Moreover, for human administration, it will be understood that preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biological Standards.

Typically, such compositions can be prepared as injectables, either as liquid solutions or suspensions solid forms suitable for preparing solutions or suspensions upon the addition of a liquid prior to injection can also be prepared and the preparations can also be emulsified. Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle that contains the basic dispersion medium and/or the other ingredients. In the case of sterile powders for the preparation of sterile injectable solutions, suspensions or emulsion, the preferred methods of preparation are vacuum-drying or freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered liquid medium thereof. The liquid medium should be suitably buffered if necessary and the liquid diluent first rendered isotonic prior to injection with sufficient saline or glucose. The preparation of highly concentrated compositions for direct injection is also contemplated, where the use of DMSO as solvent is envisioned to result in extremely rapid penetration, delivering high concentrations of the active agents to a small area. The compositions will be sterile, be fluid to the extent that easy syringability exists, stable under the conditions of manufacture and storage, and preserved against the contaminating action of microorganisms, such as bacteria and fungi. It will be appreciated that endotoxin contamination should be kept minimally at a safe level, for example, less that 0.5 ng/mg protein.

In certain aspects of the invention, the DNA methyltransferase inhibitor (e.g., siRNA molecule) may be prepared for administration by such routes as oral ingestion. In these embodiments, the solid composition may comprise, for example, solutions, suspensions, emulsions, tablets, pills, capsules (e.g., hard or soft shelled gelatin capsules), sustained release formulations, buccal compositions, troches, elixirs, suspensions, syrups, wafers, or combinations thereof. Oral compositions may be incorporated directly with the food of the diet. Preferred carriers for oral administration comprise inert diluents, assimilable edible carriers or combinations thereof. In other aspects of the invention, the oral composition may be prepared as a syrup or elixir. A syrup or elixir, and may comprise, for example, at least one active agent, a sweetening agent, a preservative, a flavoring agent, a dye, a preservative, or combinations thereof.

In some aspects of the invention an oral composition may comprise one or more binders, excipients, disintegration agents, lubricants, flavoring agents, and combinations thereof. In certain embodiments, a composition may comprise one or more of the following: a binder, such as, for example, gum tragacanth, acacia, cornstarch, gelatin or combinations thereof; an excipient, such as, for example, dicalcium phosphate, mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate or combinations thereof a disintegrating agent, such as, for example, corn starch, potato starch, alginic acid or combinations thereof a lubricant, such as, for example, magnesium stearate a sweetening agent, such as, for example, sucrose, lactose, saccharin or combinations thereof a flavoring agent, such as, for example peppermint, oil of wintergreen, cherry flavoring, orange flavoring, etc. or combinations thereof the foregoing. When the dosage unit form is a capsule, it may contain, in addition to materials of the above type, carriers such as a liquid carrier. Various other materials may be present as coatings or to otherwise modify the physical form of the dosage unit. For instance, tablets, pills, or capsules may be coated with shellac, sugar or both.

Additional formulations suitable for administration may include suppositories. Suppositories are solid dosage forms of various weights and shapes, usually medicated, for insertion into the rectum, vagina or urethra. After insertion, suppositories soften, melt or dissolve in the cavity fluids. In general, for suppositories, traditional carriers may include, for example, polyalkylene glycols, triglycerides or combinations thereof. In certain embodiments, suppositories may be formed from mixtures containing, for example, the active ingredient in the range of about 0.5% to about 10%, and preferably about 1% to about 2%.

Although it is most preferred that solutions of a delta DNA methyltransferase 3B inhibitory composition of the present invention (and/or a additional agent) be prepared in sterile water containing other non-active ingredients, made suitable for injection, solutions of such active ingredients can also be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose, if desired. Dispersions can also be prepared in liquid polyethylene glycols, and mixtures thereof and in oils. The carrier can also be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, propylene glycol, and liquid polyethylene glycol, and the like), lipids (e.g., triglycerides, vegetable oils, liposomes) and combinations thereof. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.

The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.

Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, sterile aqueous media which can be employed will be known to those of skill in the art in light of the present disclosure. Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject.

It is particularly contemplated that suitable pharmaceutical compositions will generally comprise, but are not limited to, from about 10 to about 100 mg of the desired molecule or agent admixed with an acceptable pharmaceutical diluent or excipient, such as a sterile aqueous solution, to give a final concentration of about 0.25 mg/ml to about 2.5 mg/ml with respect to the conjugate, in, for example, 0.15M NaCl aqueous solution at pH 7.5 to 9.0. The preparations may be stored frozen at −10° C. to −70° C. for at least 1 year.

X. Combination Therapy

In order to increase the effectiveness of the compositions described herein, such as inhibitors of the ΔDNMT3B variants, including siRNA, antisense RNA, antibodies, small molecules, and so forth, it may be desirable to combine these compositions with other agents effective in the treatment of hyperproliferative disease, such as anti-cancer agents. An “anti-cancer” agent is capable of negatively affecting cancer in a subject, for example, by killing cancer cells, inducing apoptosis in cancer cells, reducing the growth rate of cancer cells, reducing the incidence or number of metastases, reducing tumor size, inhibiting tumor growth, reducing the blood supply to a tumor or cancer cells, promoting an immune response against cancer cells or a tumor, preventing or inhibiting the progression of cancer, or increasing the lifespan of a subject with cancer. More generally, these other compositions would be provided in a combined amount effective to kill or inhibit proliferation of the cell. This process may involve contacting the cells with the expression construct and the agent(s) or multiple factor(s) at the same time. This may be achieved by contacting the cell with a single composition or pharmacological formulation that includes both agents, or by contacting the cell with two distinct compositions or formulations at the same time, wherein one composition includes the expression construct and the other includes the second agent(s) or in succession of one another

Tumor cell resistance to chemotherapy and radiotherapy agents represents a major problem in clinical oncology. One goal of current cancer research is to find ways to improve the efficacy of chemo- and radiotherapy by combining it with gene therapy. For example, the herpes simplex-thymidine kinase (HS-tK) gene, when delivered to brain tumors by a retroviral vector system, successfully induced susceptibility to the antiviral agent ganciclovir (Culver, et al., 1992). In the context of the present invention, it is contemplated that inhibitors of ΔDNMT3B variants could be used similarly in conjunction with chemotherapeutic, radiotherapeutic, or immunotherapeutic intervention, for example, in addition to other pro-apoptotic or cell cycle regulating agents.

Alternatively, the inventive therapy may precede or follow the other agent treatment by intervals ranging from minutes to weeks. In embodiments where the other agent and expression construct are applied separately to the cell, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the agent and expression construct would still be able to exert an advantageously combined effect on the cell. In such instances, it is contemplated that one may contact the cell with both modalities within about 12-24 h of each other and, more preferably, within about 6-12 h of each other. In some situations, it may be desirable to extend the time period for treatment significantly, however, where several d (2, 3, 4, 5, 6 or 7) to several wk (1, 2, 3, 4, 5, 6, 7 or 8) lapse between the respective administrations.

Various exemplary combinations may be employed, wherein the therapy of the present invention is “A” and the secondary agent, such as radio- or chemotherapy, is “B”:

A/B/A B/A/B B/B/A A/A/B A/B/B B/A/A A/B/B/B B/A/B/B B/B/B/A  B/B/A/B A/A/B/B  A/B/A/B A/B/B/A  B/B/A/A B/A/B/A  B/A/A/B A/A/A/B  B/A/A/A A/B/A/A  A/A/B/A

Administration of the therapeutic compositions of the present invention to a patient will follow general protocols for the administration of chemotherapeutics, taking into account the toxicity, if any, of the vector. It is expected that the treatment cycles would be repeated as necessary. It also is contemplated that various standard therapies, as well as surgical intervention, may be applied in combination with the described hyperproliferative cell therapy.

A. Chemotherapy

Cancer therapies also include a variety of combination therapies with both chemical and radiation based treatments. Combination chemotherapies include, for example, cisplatin (CDDP), carboplatin, procarbazine, mechlorethamine, cyclophosphamide, camptothecin, ifosfamide, melphalan, chlorambucil, busulfan, nitrosurea, dactinomycin, daunorubicin, doxorubicin, bleomycin, plicomycin, mitomycin, etoposide (VP16), tamoxifen, raloxifene, estrogen receptor binding agents, taxol, gemcitabien, navelbine, farnesyl-protein tansferase inhibitors, transplatinum, 5-fluorouracil, vincristin, vinblastin and methotrexate, or any analog or derivative variant of the foregoing.

In particular, the present invention may relate to providing additional therapy for treatment of NSCLC. In these instances, compositions of the present invention may be useful for combination therapy with the exemplary NSCLC chemotherapeutic agents, for example, Camptosar (irinotecan CPT-11) Camptothecin Carboplatin (Paraplatin) Cisplatin (Platinol) Epirubicin Gemzar (gemcitabine) Navelbine (vinorelbine) Oxaliplatin Taxol (paclitaxel) or Taxotere (docetaxel).

B. Radiotherapy

Other factors that cause DNA damage and have been used extensively include what are commonly known as γ-rays, X-rays, and/or the directed delivery of radioisotopes to tumor cells. Other forms of DNA damaging factors are also contemplated such as microwaves and UV-irradiation. It is most likely that all of these factors effect a broad range of damage on DNA, on the precursors of DNA, on the replication and repair of DNA, and on the assembly and maintenance of chromosomes. Dosage ranges for X-rays range from daily doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 wk), to single doses of 2000 to 6000 roentgens. Dosage ranges for radioisotopes vary widely, and depend on the half-life of the isotope, the strength and type of radiation emitted, and the uptake by the neoplastic cells.

The terms “contacted” and “exposed,” when applied to a cell, are used herein to describe the process by which a therapeutic construct and a chemotherapeutic or radiotherapeutic agent, for example, are delivered to a target cell or are placed in direct juxtaposition with the target cell. To achieve cell killing or stasis, both agents are delivered to a cell in a combined amount effective to kill the cell or prevent it from dividing.

C. Immunotherapy

Immunotherapeutics, generally, rely on the use of immune effector cells and molecules to target and destroy cancer cells. The immune effector may be, for example, an antibody specific for some marker on the surface of a tumor cell. The antibody alone may serve as an effector of therapy or it may recruit other cells to actually effect cell killing. The antibody also may be conjugated to a drug or toxin (chemotherapeutic, radionuclide, ricin A chain, cholera toxin, pertussis toxin, etc.) and serve merely as a targeting agent. Alternatively, the effector may be a lymphocyte carrying a surface molecule that interacts, either directly or indirectly, with a tumor cell target. Various effector cells include cytotoxic T cells and NK cells.

Immunotherapy, thus, could be used as part of a combined therapy, in conjunction with therapy of the present invention. The general approach for combined therapy is discussed below. Generally, the tumor cell must bear some marker that is amenable to targeting, i.e., is not present on the majority of other cells. Many tumor markers exist and any of these may be suitable for targeting in the context of the present invention. Common tumor markers include carcinoembryonic antigen, prostate specific antigen, urinary tumor associated antigen, fetal antigen, tyrosinase (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, MucB, PLAP, estrogen receptor, laminin receptor, erb B and p155.

D. Genes

In yet another embodiment, the secondary treatment is a gene therapy in which a therapeutic polynucleotide is administered before, after, or at the same time as the therapy provided by the present invention. Delivery of a composition of the present invention in conjuction with a vector encoding a therpeutic gene product will have a combined anti-hyperproliferative effect on target tissues. Alternatively, a single vector encoding both genes may be used. A variety of proteins are encompassed within the invention, including inhibitors of cellular proliferation, such as p53, p16, C-CAM, Rb, APC, DCC, NF-1, NF-2, WT-1, MEN-I, MEN-II, zac1, p73, VHL, MMAC1/PTEN, DBCCR-1, FCC, rsk-3, p27, p27/p16 fusions, p21/p27 fusions, anti-thrombotic genes (e.g., COX-1, TFPI), PGS, Dp, E2F, ras, myc, neu, raf, erb, fms, trk, ret, gsp, hst, abl, E1A, p300, genes involved in angiogenesis (e.g., VEGF, FGF, thrombospondin, BAI-1, GDAIF, or their receptors) and MCC, for example and regulators of programmed cell death, such as a Bcl 2 family member (e.g., BclXL, BclW, BclS, Mcl-1, A1, Bfl-1) or counteract Bcl 2 function and promote cell death (e.g., Bax, Bak, Bik, Bim, Bid, Bad, Harakiri).

E. Surgery

Approximately 60% of persons with cancer will undergo surgery of some type, which includes preventative, diagnostic or staging, curative and palliative surgery. Curative surgery is a cancer treatment that may be used in conjunction with other therapies, such as the treatment of the present invention, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy and/or alternative therapies.

Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed. Tumor resection refers to physical removal of at least part of a tumor. In addition to tumor resection, treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and miscopically controlled surgery (Mohs' surgery). It is further contemplated that the present invention may be used in conjunction with removal of superficial cancers, precancers, or incidental amounts of normal tissue.

Upon excision of part of all of cancerous cells, tissue, or tumor, a cavity may be formed in the body. Treatment may be accomplished by perfusion, direct injection or local application of the area with an additional anti-cancer therapy. Such treatment may be repeated, for example, every 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 months. These treatments may be of varying dosages as well.

F. Other Agents

It is contemplated that other agents may be used in combination with the present invention to improve the therapeutic efficacy of treatment. These additional agents include immunomodulatory agents, agents that affect the upregulation of cell surface receptors and GAP junctions, cytostatic and differentiation agents, inhibitors of cell adehesion, or agents that increase the sensitivity of the hyperproliferative cells to apoptotic inducers. Immunomodulatory agents include tumor necrosis factor interferon alpha, beta, and gamma IL-2 and other cytokines F42K and other cytokine analogs or MIP-1, MIP-1beta, MCP-1, RANTES, and other chemokines. It is further contemplated that the upregulation of cell surface receptors or their ligands such as Fas/Fas ligand, DR4 or DR5/TRAIL would potentiate the apoptotic inducing abililties of the present invention by establishment of an autocrine or paracrine effect on hyperproliferative cells. Increases intercellular signaling by elevating the number of GAP junctions would increase the anti-hyperproliferative effects on the neighboring hyperproliferative cell population. In other embodiments, cytostatic or differentiation agents can be used in combination with the present invention to improve the anti-hyerproliferative efficacy of the treatments. Inhibitors of cell adehesion are contemplated to improve the efficacy of the present invention. Examples of cell adhesion inhibitors are focal adhesion kinase (FAKs) inhibitors and Lovastatin. It is further contemplated that other agents that increase the sensitivity of a hyperproliferative cell to apoptosis, such as the antibody c225, could be used in combination with the present invention to improve the treatment efficacy.

Hormonal therapy may also be used in conjunction with the present invention or in combination with any other cancer therapy previously described. The use of hormones may be employed in the treatment of certain cancers such as breast, prostate, ovarian, or cervical cancer to lower the level or block the effects of certain hormones such as testosterone or estrogen. This treatment is often used in combination with at least one other cancer therapy as a treatment option or to reduce the risk of metastases.

XI. EXAMPLES

The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Example 1 Experimental Procedures

Study population. One hundred nineteen patients who were diagnosed with pathologic stage I-IIIA NSCLC and had undergone lobectomy or pneumonectomy for complete resection of their primary tumors at The University of Texas M. D. Anderson Cancer Center between 1994 and 2001 were included in the study. The selection of these patients was based on available fresh tumor tissues and corresponding normal lung tissues. The clinical information and follow-up data were based on chart review and on reports from the tumor registry service. Informed consent for the use of residual resected tissues for research was obtained from all the patients in the study. The study was reviewed and approved by the institution's Surveillance Committee. None of the patients with stages I or II disease received adjuvant chemotherapy or radiotherapy before or after surgery. Among 49 patients with stage IIIA disease, 5 received preoperative chemotherapy or chemo-radiotherapy, 20 received postoperative concurrent chemo-radiotherapy, 17 received postoperative radiotherapy alone, and 2 received postoperative chemotherapy alone, and 5 received no additional treatment.

DNA extraction and methylation-specific polymerase chain reaction. Frozen tumor tissues and corresponding distant normal lung tissues were homogenized, and genomic DNA was extracted by digestion of the homogenized tissues in a buffer containing 50 mM Tris-HCl (pH 8.0), 1% sodium dodecyl sulfate, and 0.5 mg/ml proteinase K at 42° C. for 36 h. The digested products were purified with phenyl-chloroform twice. DNA was then precipitated using the ethanol precipitation method and recovered in distilled DNase-free water.

For the methylation-specific polymerase chain reaction (MSP), 1 μg of genomic DNA from each tissue sample was used in the initial step of chemical modification. Briefly, DNA was denatured by NaOH and treated with sodium bisulfite (Sigma Chemical Co., St. Louis, Mo.). After purification with Wizard DNA purification resin (Promega Corp., Madison, Wis.), the DNA was treated again with NaOH. After precipitation, DNA was recovered in water and was prepared for polymerase chain reaction (PCR™) using specific primers for either the methylated or the unmethylated p16^(INK4a) or RASSF1A promoter: p16-MAS (5′-ACCCGAC-CCCGAACCGCGACCGTAA-3′SEQ ID NO:30) and p16-MS (5′-TTATTAGAGGGTGGGGCGGATCG-CGTGC-3′SEQ ID NO:31) for the methylated p16^(INK4a) promoter p16-UAS (5′-CAACCCCAAACCACAA-CCATAA-3′SEQ ID NO:32) and p16-US (5′-TTATTAGAGGGTGGGGTGGATTGT-3′SEQ ID NO:33) for the unmethylated p16^(INK4a) promoter RASSF1A-MAS (5′-GCTAACAAACGCGAACCG-3′SEQ ID NO:34) and RASSF1A-MS (5′-GGGTTTTGCGAGAGCGCG-3′SEQ ID NO:35) for the methylated RASSF1A promoter and RASSF1A-UAS (5′-CACTAACAAACACAAACC-3′SEQ ID NO:36) and RASSF1A-US (5′-GGTTTTTGTGAGAGTGTGTT-TAG-3′SEQ ID NO:37) for the unmethylated RASSF1A promoter. PCR™ was carried out in 25 μl containing about 100 ng of modified DNA, 3% dimethyl sulfoxide, all four deoxynucleoside triphosphates (each at 200 μM), 1.5 mM MgCl₂, 0.4 μM PCR™ primers, and 1.25 U of HotStarTaq DNA polymerase (Qiagen, Inc., Valencia Calif.). DNA was amplified in 500-μl plastic tubes for 35 cycles at 95° C. for 30 seconds, 56-64° C. for 60 seconds, and 70° C. for 60 seconds followed by a 5-minute extension at 70° C. in a temperature cycler (Hybaid Omnigene, Woodbridge, N.J.). PCR™ products were separated on 2.5% agarose gels and visualized after staining with ethidium bromide. For each DNA sample, primer sets for methylated DNA and unmethylated DNA were used for analysis. CpGenome™ universal methylated DNA (Chemicon International, Temecula, Calif.) was used as a positive control, and water replacing for DNA was used as blank controls. The hypermethylation status was determined by visualizing a 150-bp PCR™ product for the p16^(INK4a) promoter and a 169-bp PCR™ product for the RASSF1A promoter with the respective methylation-specific primer sets. All PCRs were repeated twice, and the results were reproducible.

Statistical analysis. The χ² test or Fisher's exact test were used to test the association between categorical variables. The Cochran-Armitage trend test was used to test the trend of methylation among differentiation levels. Overall survival, disease-specific survival (i.e., survival rates among people who died of lung cancer-related causes specifically), and disease-free survival (i.e., recurrence, metastasis, or cancer death was considered an event) were analyzed. Survival probability was estimated using the Kaplan-Meier method. The log-rank test was used to compare survival times among groups. Cox regression was used to model the risks of p16^(INK4a) and/or RASSF1A promoter hypermethylation on survival time, with adjustment for clinical and histopathologic parameters (age, sex, tumor histology, tumor size, smoking status, and adjuvant treatment). All statistical tests were two-sided, and P<0.05 was considered statistically significant.

Cell Lines and Primary Tissues. Human NSCLC lines H157, H226, H292, H358, H460, H522, H596, H1299, H1792, H1944, Calu-6, SK-MES, and A549 were purchased from the American Type Cell Culture (Rockville, Md.). Cells were cultured in DMEM supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mM L-glutamine, 100 IU/ml penicillin, and 100 mg/ml streptomycin at 37° C. in the presence of 5% CO₂.

One hundred and nine paired primary tumor tissues and corresponding normal lung tissues from patients with primary NSCLC were obtained from surgically resected specimens collected in the Department of Pathology at The University of Texas M. D. Anderson Cancer Center and stored at −80° C. until the experiment. The study was approved by the Institutional Review Boards in The University of Texas M. D. Anderson Cancer Center.

RNA Extraction and RT-PCR. Total RNA for each cell line and clinic sample was isolated using Tri-Reagent (Molecular Research Center, Inc., Cincinnati, Ohio) according to manufacturer's instruction. Approximately 1 μg of total RNA from each sample was used to conduct reverse transcription reaction in a 20 μl volume using Superscript II RNase H-reverse transcriptase (GibcoBRL Life Technologies Inc., Grand Island, N.Y.). The synthesized cDNA was either used immediately for PCR™ amplification or stored at −20° C. for further analysis.

The mRNA expression level of total DNMT3Bs was detected by using primer set of the forward primer S1 (5′-GAGTTGGGCATAAAGGTAGG-3′SEQ ID NO:38) and the reverse primer 1AS1 (5′-TGAGGTACACGGTATGACC-3′SEQ ID NO:39) located at exon 17 and 3′-untranslation region of DNMT3B1, respectively. The 5′-end forward primers E1 (5′-CATGAAGGGAGACACCAGGC-3′SEQ ID NO:40), E3 (5′-ATGCCAAAGCTCTTCCGGGA-3′SEQ ID NO:41), E5 (5′-TGGAGATGGAGACAGTTCAG-3′SEQ ID NO:42), and the reverse primer 1AS1 were further used to detect DNMT3Bs (FIG. 9A).

PCR™ reaction was performed in a 12.5 μl volume containing 0.5 μl RT products, 7% DMSO, 1.5 mM dNTPs, 6.7 mM MgCl₂, 16.6 mM (NH₄)₂SO₄, 67 mM Tris, 10 mM β-mercaptoethanol, 6.7 μM EDTA, 0.5 μM of both the forward and the reverse primer, and 0.625 unit of HotStar Taq DNA polymerase (Qiagen, Inc., Chatsworth, Calif.). Amplification was carried out with an initial denaturing step at 95° C. for 15 min, followed by 35 cycles of 95° C. for 30 s, 58-62° C. for 1 min, and 72° C. for 1 min in a thermal cycler (Hybaid PCR™ Express, Middlesex, UK) with a last extension step of 72° C. for 10 min. The PCR™ products were mixed with 6× loading buffer containing 0.5 mg/ml of ethidium bromide and separated by electrophoresis on a 2% agarose gel.

Primer Extension and Nuclease S1 Mapping. To determine the exact starting site of ΔDNMT3B transcript, the standard primer extension and S1 mapping methods were used with the γ-³²P-ATP end-labeled antisense primer 3B6AS (5′-GGTAGCCGGGAACTCCACGG-3′SEQ ID NO:43). For primer extension, briefly, 1 μg of total RNA was mixed with ³²P-labelled primer. The mixture was incubated at 70° C. for 15 minutes and following at room temperature for 10 min, respectively. Extension reactions (20 μl) consisted of 50 mM Tris (pH 8.3), 75 mM KCl, 3 mM MgCl₂, 10 mM dithiothreitol, 1 mM each dNTP, and 200 U SuperScript™II reverse transcriptase (GibcoBRL Life Technologies Inc., Grand Island, N.Y.). Reactions were incubated at 37° C. for 15 min. The products were mixed with loading buffer (95% formamide, 20 mM EDTA, 0.05% bromophenol blue and 0.02% xylene cyanole FF), denatured at 98° C. for 5 minutes, and then separated on a 12% acrylamide-7 M urea denatured gel. Radioactive signals were detected by autoradiography.

Nuclease S1 mapping was performed with a 1080 bp DNA fragment which was amplified using the forward primer E4INT-1 (5′-TGCTGTGACAGGCAG AGCAG-3′; SEQ ID NO:44) and the reverse primer ESAS (5′-TCTGTGTCGTCTGTGAGGTC-3′SEQ ID NO:45). After cloned this fragment into PCR®2.1-TOPO® vector (Invitrogen Corp., Carlsbad, Calif.), a 320 bp fragment of single strand DNA probe used for S1 nuclease mapping was generated by single-primer PCR™ using ³³P-labelled internal primer 3B6AS. The PCR™ condition was same as above. This single-strand 320 bp PCR™ product was separated in a 2% agarose gel and purified using QIAquick gel extraction kit (QIAGEN Inc., Chatsworth, Calif.) followed by recovering in 50 μl Tris buffer (10 mM Tris.Cl, pH8.5).

Total RNA from different samples was co-precipitated with 50 ng of recovered 320 bp ³³P-labelled probe. Samples were dissolved in 30 μl of hybridization buffer (40 mM MOPS, pH 6.4, 1 mM EDTA, 0.4 M NaCl and 80% formamide) and incubated at 85° C. for 15 min. After hybridization for overnight at 54° C. based on the GC content of the projected fragment, the samples were digested for 1 h at 37° C. with S1 nuclease (GibcoBRL Life Technologies Inc., Grand Island, N.Y.) in the buffer containing 30 mM sodium acetate, pH 4.6, 1 mM zinc acetate, 5% glycerol, and 0.28 M NaCl. The resulting products were detected as described in primer extension section.

Construction of ΔDNMT3B Promoter and Luciferase Assay. The putative 1080 bp ΔDNMT3B promoter was amplified with primer set of E4INT-1 and E5AS. This fragment contains upstream 355-bp from ΔDNMT3B transcription starting site, first exon and first intron of ΔDNMT3B. After inserting the fragment into pGL3-basic vector (Promega Corp., Madison, Wis.), plasmids containing both forward (F) and reverse (R) directions of the insert were used for transient transfection.

A549 and H157 were used for transient transfection using FuGENE 6 Transfection Reagent (Roche Diagnostics Corp., Indianapolis, Ind.) according to protocol of the manufacturer. The plasmid pCH110 (Amersham Pharmacia Biotech, Inc., Piscataway, N.J.) was used as an internal control to monitor transfection efficiency. The signal was detected using a Luciferase Assay System (Promega Corp., Madison, Wis.) in a luminometer (Lumat LB 9507) (Berthold, Oak Ridge, Tenn.). The values of luciferase activity were normalized against those of β-galactosidase expressed by plasmid pCH110.

Detection of individual ΔDNMT3B Splicing Variants. The expression levels of specific DNMT3B and ΔDNMT3B variants in NSCLC cell lines and primary tissues were determined by using specific primer sets corresponding to individual DNMT3B or ΔDNMT3B variants. For ΔDNMT3B1, the inventors used 1S, 5′-TGGAAGGCCACCTCCAAGC-3′ (SEQ ID NO:46), as the forward primer and 1AS, 5′-GCCTGCACGACGCACCTTCG-3′ (SEQ ID NO:47), as the reverse primer for ΔDNMT3B2, 2S, 5′-AGATCAAGGGCTTCTCCTGG-3′ (SEQ ID NO:48), as the forward primer and 2AS, 5′-GAGTCTTGTTCTCTGGTTGCG-3′ (SEQ ID NO:49), as the reserves primer for ΔDNMT3B3, 3S, 5′-GTTCAGAGTATCAGGTCTCTGC-3′ (SEQ ID NO:50), as the forward primer and 1AS as the reverse primer for ΔDNMT3B4, 3S as the forward primer and 2AS as the reverse primer; for ΔDNMT3B5, 4S, 5′-GTTCAGAGTATCAGAGAACAAGAC-3′ (SEQ ID NO:51), as the forward primer and 3AS, 5′-CTGCCACAAGACAAACAGCC-3′ (SEQ ID NO:52), as the reverse primer for ΔDNMT3B6, 5S, 5′-GTTCTCCGAGAGAACAAGAC-3′ (SEQ ID NO:53), as the forward primer and 4AS, 5′-CAGTAAGACTGATAGCCATCG-3′ (SEQ ID NO:54), as the reverse primer for ΔDNMT3B7, 6S, 5′-TGCTCTGGAGAGAACAAGAC-3′ (SEQ ID NO:55), as the forward primer and 5AS, 5′-GAGACACATGTAACAGCTCC-3′ (SEQ ID NO:56), as the reverse primer. A common forward primer E1, 5′-TGCTAAGCTACACACAGGAC-3′ (SEQ ID NO:57), was used for DNMT3B variants and specific reverse primers were used to distinguish individual variants as following: 1AS for DNMT3Bs corresponding to ΔDNMT3B1 and ΔDNMT3B3 2AS for DNMT3Bs corresponding to ΔDNMT3B2 and ΔDNMT3B4 6AS, 5′-CGAGTCTTGTTCTCTGATACTC-3′ (SEQ ID NO:58), for DNMT3B corresponding to ΔDNMT3B5 7AS, 5′-CGAGTCTTGTTCTCTCGGAG-3′ (SEQ ID NO:59), for DNMT3B corresponding to ΔDNMT3B6; and 8AS, 5′-CGAGTCTTGTTCTCTCCA G-3′ (SEQ ID NO:60), for DNMT3B corresponding to ΔDNMT3B7.

DNA extraction and MSP. Frozen tumor tissues and corresponding distant normal lung tissues were homogenized and genomic DNA was extracted by digestion of homogenized tissues in buffer containing 50 mM Tris-HCl (pH 8.0), 1% sodium dodecyl sulfate, and 0.5 mg/ml proteinase K at 42° C. for 36 h. The digested products were purified with phenyl-chloroform twice. DNA was then precipitated using the ethanol precipitation method and recovered in distilled DNase-free water. For MSP, 1 μg of genomic DNA from each tissue sample was used in the initial step of chemical modification. Briefly, DNA was denatured by NaOH and treated with sodium bisulfite (Gigma Chemical Co., St. Louis, Mo.). After purification with the use of Wizard DNA purification resin (Promega Corp., Madison, Wis.), the DNA was treated again with NaOH. After precipitation, DNA was recovered in water and was ready to add to a polymerase chain reaction (PCR™) with the use of specific primers for either the methylated or the unmethylated p16^(INK4a) or RASSF1A promoter, as described previously (Soria et al., 2002). PCRs were carried out in 25 μL containing about 100 ng of modified DNA, 3% dimethyl sulfoxide, all four deoxynucleoside triphosphates (each at 200 μM), 1.5 mM MgCl₂, 0.4 μM PCR™ primers, and 1.25 U of Taq DNA polymerase (Life Technologies, Inc., Gaithersburg, Md.). DNA was amplified for 35 cycles at 95° C. for 30 seconds, 60° C. for 60 seconds, and 70° C. for 60 seconds, followed by a 5-minute extension at 70° C. in a temperature cycler (Hybaid Omnigene, Woodbridge, N.J.) in 500 μL plastic tubes. PCR™ products were separated on 2.5% agarose gels and visualized after staining with ethidium bromide. For each DNA sample, primer sets for methylated DNA and unmethylated DNA were used for analysis. CpGenome™ universal methylated DNA (Chemicon International, Temecula, Calif.) was used as positive controls, and water replacing for DNA was used as blank controls. CpGenome™ universal methylated DNA (Chemicon International, Temecula, Calif.) was used as positive controls, and water replacing for DNA was used as blank controls. The hypermethylation status was determined by visualizing a 150-base-pair PCR™ product for p16^(INK4a) and a 167-base-pair PCR™ product for RASSF1A with the respective methylation-specific primer sets. All PCRs were repeated twice, and the results were reproducible.

siRNA and antisense RNA transfection. siRNA specifically targeting to the junction of exon 5 and 7 of ΔDNMT3B were designed based on principles published previously (Elbashir et al., 2001) and synthesized chemically (Ambion). Both annealed siRNA and corresponding oligonucleotides of single strands were ordered and exemplary sequences were as follows: sense strand: 5′-CACGCAACCAGAGAACAAGUU-3′ (SEQ ID NO:61); antisense strand: 5′-CUUGUUCUCUGGUUGCGUGUU-3′ (SEQ ID NO:62). An exemplary target sequence for annealed siRNA is as follows: 5′-AACACGCAACCAGAGAACAAG (SEQ ID NO:63). siRNA specifically targeting GAPDH and siRNA negative (scramble) control were also purchased from Ambion. Briefly, a defined number of cells (5×10⁵) were incubated in 6 well plastic plates for 12-24 h in DMEM with 10% FCS to achieve 60-70% cell confluence before transfection. Different concentrations of ΔDNMT3B-specific siRNA (10 nM to 80 nM), antisense oligo-dioxynucleotide (40 nM), 40 nM GAPDH-positive or negative siRNA, or medium alone were mixed with Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions and added into each well in serum-free condition. After transfection for 4 h at 37° C., cells were washed with phosphate-buffered saline (PBS) and cultivated in DMEM medium that contained 10% FCS. At 12, 24, 48, and 72 h after transfection, cells were harvested and stored at −80° C. until the time of RNA, DNA and protein extraction.

Bisulfite sequencing of RASSF1A promoter. MSP products from isolated genomic DNAs treated with either 40 nM siRNA-GAPDH or 40 nM siRNA-ΔDNMT3B4/2 were gel-purified using QIAquick gel extraction kit (QIAGEN Inc., Chatsworth, Calif.) followed by recovering in 50 μl Tris buffer (10 mM Tris Cl, pH 8.5) and then cloned into a TA cloning vector (Invitrogen). Inserts in individual plasmid molecules were then sequenced using the ABI PRISM 377 DNA Sequencer (Perkin-Elmer, Foster City, Calif.).

Western blotting. Cells treated by siRNA were washed once with PBS and collected by scraping in 200 μl of lysis buffer [50 mM HEPES, 0.5 M sodium chloride, 1.5 mM magnesium chloride, 1 mM EGTA, 10% (v/v) glycerol, 1% Triton X-100, and 5 μl/ml of Protease Inhibitor Cocktail (Sigma)]. The lysates were incubated on ice for 1 h with intermittent vortexing followed by centrifugation at 40,000 g for 10 min at 4° C. Equal amounts of protein from each treatment group were diluted with loading buffer, boiled, and loaded onto 7.5% SDS-polyacrylamide gel. Samples were electrophoresed at 150 to 180 V for 3 to 4 h, and separated proteins were transferred to polyvinylidene fluoride membrane. Proteins were detected by incubation with antibodies against DNMT1 (BD Biosciences) followed by blotting with horseradish peroxidase-conjugated anti-mouse secondary antibody (Sigma). Signals were then detected using a ECL Western blotting detection kit (Amersham, Piscataway, N.J.).

Statistical analysis of DNMT3B data. Summary statistics, including frequency tabulation, means, standard deviations, median, and range, were given to characterize subject characteristics and the expression of ΔDNMT3B variants. The chi-square (χ²) test or Fisher's exact test was used to test the association between two categorical variables. The McNemar's test was used to test changes in any ΔDNMT3B variants between tumor tissue and adjacent normal tissue. The logistic model was applied to model the association between ΔDNMT3B variants and p16^(INK)4a and RASSF1A promoter methylation. All statistical tests were two-sided, with a 5% type I error rate. Statistical analysis was performed with standard statistical software, including SAS Release 8.1 (SAS User Guide, Cary, N.C.) and S-Plus 2000 (S-plus 2000 Guide to Statistics, Mathsoft, Inc., Seattle, Wash.).

Example 2 Clinical Characterization of Patients

Clinical characteristics of all patients enrolled in the study are summarized in Table 2. Among the 119 patients, 47 (39%) were female and 72 (61%) were male. The mean age (±standard deviation) of the population was 64.3±10.1 years (range, 39-84 years). At the censor date of Nov. 14, 2003, the median follow-up period was 51 months (range, 16-130 months). Of the 70 patients with stage I or II disease, 29 (41%) were still alive, 35 (50%) died of lung cancer, and 6 (9%) died of unrelated causes. No significant difference in 5-year overall, disease-specific, and disease-free survival rates were observed by tumor stage, gender, smoking status, differentiation status, and histologic subtype in this patient group. Among the 49 patients with stage IIIA disease, 18 (37%) were still alive, 29 (59%) died of lung cancer, and 2 (4%) died of unrelated causes. In this group of patients, smokers had significantly poorer 5-year survival rates than the non-smokers did (P=0.047, P=0.03, and P=0.03 for 5-year overall, disease-specific, and disease-free survival rates, respectively). Thirty-five (71%) of the 49 patients received postoperative radiotherapy with (26 patients, including 5 with preoperative chemotherapy) or without (9 patients) concomitant chemotherapy, while 14 patients received no adjuvant therapy after surgery.

TABLE 2 Characteristics of Patents and Tumors P16^(INK4a) Promoter RASSF1A Promoter Methylation Methylation Absent Present Absent Present Total Patients 58 (49%) 61 (51%) 73 (61%) 46 (39%)  119 (100%) Gender* Female 23 (49%) 24 (51%) 33 (70%) 14 (30%)  47 (39%) Male 38 (53%) 34 (47%) 40 (56%) 32 (44%)  72 (61%) Mean age (± standard 65.0 ± 10.9 yr 63.5 ± 9.1 yr 65.1 ± 10.2 yr 63.0 ± 9.9 yr 64.3 ± 10.1 yr deviation) Smoking status Non-smoker 22 (58%) 16 (42%) 25 (66%) 13 (34%)  38 (32%) Smoker 39 (48%) 42 (52%) 48 (59%) 33 (41%)  81 (68%) Histologic type Adenocarcinoma 34 (57%) 26 (43%) 40 (67%) 20 (33%)  60 (50%) Squamous cell 23 (47%) 26 (53%) 27 (55%) 22 (45%)  49 (41%) carcinoma Large cell carcinoma  2 (29%)  5 (71%)  6 (86%)  1 (14%)  7 (6%)  Other  2 (67%)  1 (33%)  0 (0%)   3 (100%)  3 (3%)  Differentiation** Well  5 (45%)  6 (55%)  9 (82%)  2 (18%)  11 (9%)  Moderate 25 (50%) 25 (50%) 32 (64%) 18 (36%)  50 (42%) Poor 31 (53%) 27 (47%) 32 (55%) 26 (45%)  58 (49%) Stage I & II 37 (53%) 33 (47%) 42 (60%) 28 (40%)  70 (59%) IIIA 24 (94%) 25 (51%) 31 (63%) 18 (37%)  49 (41%) Stage I & II, 5-year 61.7% 28.3% 50.6% 41.1% 46.5% overall survival Stage III, 5-year 53.5% 10.8% 45.6%   0% 30.8% overall survival *Subset analysis indicated that male patients had a higher rate of RASSF1A promoter methylation than females in stage IIIA group (P-0.03). **Subset analysis indicated that poorly differentiated tumors had a higher rate of RASSF1A promoter methylation than well or moderately differentiated tumors in stage IIIA group (P = 0.04).

Example 3 Determining Methylation Status of Promoters

Using MSP, the methylation status of the p16^(INK4a) and RASSF1A promoters in 119 primary tumors and the corresponding normal-appearing lungs was determined (FIG. 1). Promoter methylation was detected in 58 (49%) and 46 (39%) of the tumor tissue for the p16^(INK4a) and RASSF1A promoters, respectively, compared with 13 (11%, including 4 samples whose corresponding tumors lacked methylation of the p16^(INK)4a promoter), and 4 (3%) in the corresponding normal-appearing lung tissues (P<0.0001). Unmethylated promoters of p16^(INK4a) and RASSF1A were detected in all the normal-appearing lung tissues, and in 60% of tumor tissues, most likely because of the presence of normal cells in the tumor samples. In patients with stage I or II NSCLC, tumors with methylation of the p16^(INK4a) promoter had a higher frequency of RASSF1A promoter methylation than those without p16^(INK4a) promoter methylation, 58% versus 24% (P=0.005), suggesting that RASSF1A promoter methylation tends to occur in tumors with p16^(INK4a) promoter methylation since RASSF1A promoter methylation occurs late in lung carcinogenesis (Belinsky et al., 2002) and Mao et al. unpublished data). However, this association was not significant in tumors from patients with stage IIIA disease (44% versus 29%; P=0.28). Altogether, 30 tumors (25% 19 stage I/II stage IIIA) showed concomitant methylation of both p16^(INK4a) and RASSF1A promoters.

Example 4 Association Between Methylation Status and Other Patient Characteristics

The potential association between the methylation status of p16^(INK4a) and RASSF1A promoters and sex, age, smoking history, histology, differentiation, and tumor stage was analyzed. RASSF1A promoter methylation was more frequently observed in poorly differentiated tumors (50%) than in moderately differentiated (26%) or in well-differentiated tumors (0% P=0.04) from patients with stage IIIA NSCLC, but there was no such association in tumors from patients with stage I/II disease (P=0.48). Additionally, tumors from male patients with stage IIIA NSCLC exhibited a significantly higher frequency of RASSF1A promoter methylation (47%) than did those from female patients (13% P=0.03). No significant association was observed between the methylation status and the other parameters analyzed.

Example 5

Effect of Promoter Methylation on Patient Survival

The effect of p16^(INK4a) and RASSF1A promoter methylation on patients' survival was also analyzed. Because stage IIIA patients often received adjuvant treatment after surgery while stage I/II patients received only surgery, the two groups separately were analyzed. In the stage I/II group, patients whose tumors contained p16^(INK4a) promoter methylation had significantly poorer 5-year overall, disease-specific, and disease-free survival rates (P=0.002, P=0.0005, and P=0.0066, respectively) than did patients whose tumors had no p16^(INK4a) promoter methylation (FIG. 2A-2C). However, the association between the RASSF1A promoter methylation status and 5-year survival rates was not significant (P=0.09, P=0.07, and P=0.07, respectively) (FIG. 2D-2F), although patients whose tumors carried RASSF1A promoter methylation performed poorer. Multivariate analysis, included clinical parameters and promoter methylation status, indicated that p16^(INK4a) promoter methylation was the only independent predictor of 5-year overall, disease-specific, and disease-free survivals. In patients with stage IIIA disease, in contrast to those with stage I/II tumors, the RASSF1A promoter methylation status was strongly associated with 5-year overall, disease-free, and disease-specific survivals (P<0.0001, P<0.0001, and P=0.0006, respectively FIG. 3A-3C), as was the p16INK4a promoter methylation status (P=0.003, P=0.002, and P=0.01, respectively, for 5-year overall, disease-specific, and disease-free survival rates FIG. 3D-3F). Although both RASSF1A and p16^(INK4a) promoter methylation status were independent predictors of survival, RASSF1A was a stronger predictor for 5-year overall, disease-specific, and disease-free survival (hazard ratio=4.76, P<0.0001; hazard ratio=6.29, P<0.0001; and hazard ratio=3.41, P=0.0007 versus hazard ratio=2.89, P=0.007; hazard ratio=3.16, P=0.005, and hazard ratio=2.36, P=0.02, respectively).

Example 6 Effect of RASSF1A Inactivation on Tumors

To determine whether RASSF1A inactivation might have an added biologic value in patients whose tumors also carried p16^(INK4a) promoter methylation, the 5-year survival rates of the group whose tumors had methylation of both genes' promoters were analyzed. In patients with stage I/II disease, the 5-year survival rates of patients whose tumors had methylation of both genes' promoters were significantly worse than in patients whose tumors had no promoter methylation or methylation of only one gene's promoter (P=0.01, P=0.005, and P=0.005, respectively, for 5-year overall, disease-specific, and disease-free survival rates; FIG. 4A-4C). Although the number of patients was small in the stage IIIA group, the association between patients whose tumors had methylation of both genes' promoters and poor survivals was striking (FIG. 4D-4F). All 11 patients (100%) in this category died of lung cancer within 3 years after surgery, while 13 (62%) of the 21 stage IIIA patients whose tumors had methylation of only one gene's promoters died of lung cancer in 5 years, and only 5 (29%) of the 17 patients whose tumors had no promoter methylation died of lung cancer in 6.5 years (P<0.0001 by log-rank test FIG. 4F).

Because 35 (71%) of the 49 patients with stage IIIA tumors received postoperative radiotherapy and 26 (53%) of the patients received adjuvant chemotherapy, it was determined whether these treatments had affected the predictive value of the methylation markers. Despite the small sample size, RASSF1A promoter methylation status remained a predictor of overall survival in radiotherapy and non-radiotherapy groups (P=0.0004 and P=0.008, respectively, for overall survival) as well as in chemotherapy and non-chemotherapy groups (P=0.001 and P=0.01, respectively, for overall survival).

Example 7 Identification of ΔDNMT3B

To determine expression levels of DNMT3B1 in normal lung tissues and lung cancer tissues, 12 pairs of primary NSCLC tissues were analyzed and matched to adjacent normal lung tissues using RT-PCR with a set of primers located at exon 17 and exon 23 of DNMT3B1 respectively. Expression of DNMT3B1 was found to be either undetectable or at trace level in the vast majority of the normal lung tissues analyzed while high expression was detected in 6 (50%) of the 12 tumors. To validate the finding, several additional sets of primers were designed that allow for the amplification of DNMT3B1 mRNA at different exon locations closer to the transcriptional initiation site of the gene.

It became evident that the expression level of the gene was much lower when a primer located at exon 2 (E1) or a primer located exon 4 (E4) was used compared to the expression level when a primer located at exon 6 (E5) of DNMT3B1 was used as a sense primer (FIG. 5A), suggesting the presence of additional transcripts which exclude exons 2 to 4. To confirm this observation, other primer sets at these regions were tested and the results were found to be consistent with the previous observation (data not shown). To exclude the possibility of contamination with homologue molecules in the RT-PCR products, each of the RT-PCR products were sequenced. The sequences matched perfectly to the originally reported DNMT3B1 sequence (GenBank accession number (AN): AL035071; SEQ ID NO:64).

To determine the exact start point(s) of the novel transcriptions, a primer extension assay was performed with RNA templates from lung cancer tissues and NSCLC cell lines using a primer (3B6AS) located at exon 5 of DNMT3B1. Two major transcriptional initiation sites located at nt 46502 and nt 46506 within exon 5 of DNMT3B1 (GenBank AN: AL035071; SEQ ID NO:64) were detected, respectively (FIG. 5B). This partial exon 5 was then named as the first exon of the novel transcript containing either 28-bp or 24-bp depending on which transcriptional initiation site it derives from. The initiation sites were validated using nuclease S1 RNA mapping analysis (data not shown). The new transcript from these starting sites was designated as ΔDNMT3B because it lacked 5 prime exons of DNMT3B.

Example 8 Characterization of ΔDNMT3B Promoter

To determine the existence of a potential promoter upstream of the newly identified transcript, a 1080 bp-DNA fragment containing the upstream 355-bp from a ΔDNMT3B transcriptional initiation site, exon 1, intron 1, and partial exon 2 of ΔDNMT3B was constructed into a vector containing a reporter gene. The forward DNA fragment demonstrated a stronger promoter activity than the reverse DNA fragment. Serial plasmids with both forward and reverse sequences of the DNA fragment with various deletions were constructed. Using these constructs, it was shown that a core 477-bp sequence (SEQ ID NO:68 and SEQ ID NO:69) between 502-bp and 26-bp upstream of the ΔDNMT3B transcription initiation site is the critical region maintaining the promoter activity (FIG. 6A). Interestingly, a common thymidine (T)/cytosine (C) polymorphism was found in the promoter region of ΔDNMT3B located at 286-bp upstream from the ΔDNMT3B transcriptional initiation site, which changes a consensus TFIID (CTCTATTCCA SEQ ID NO:65) binding site to a GATA-1 (TCTATC SEQ ID NO:29) binding site. The promoter comprising the T nucleotide is provided in SEQ ID NO:68, and the promoter comprising the C nucleotide is provided in SEQ ID NO:69. A stronger promoter activity was detected with the T allele than the C allele (18-fold vs. 12-fold compared to the control, respectively) (FIG. 6B), suggesting the genome carries T allele may be subject to higher expression of ΔDNMT3B.

Example 9 Expression of ΔDNMT3B Variants in NSCLC Cell Lines and in Primary NSCLC

During the studies, it was noted that the presence of various sizes of RT-PCR products using a single pair of primers (E5 and AS-B1, FIG. 5A) for proximal exons, suggesting the presence of splicing variants (FIG. 7A). By sequencing analysis, it was found that the transcripts initiated from this novel promoter may generate at least 7 transcriptional variants through inclusion or exclusion of different combinations of exons 3, 4, 5, and 6 of ΔDNMT3B, designated as ΔDNMT3B1-7 (FIG. 7B, SEQ ID NOS:1-7). The predicted translation of ΔDNMT3B is at position 194, where a good kozak consensus sequence presents (Kozak, 1987a; Kozak, 1987b Kozak, 1989), from the transcription initiation site. A comparative analysis of the putative amino acid sequences derived from the variants show that ΔDNMT3B lacks 200 amino acids at the N-terminal compared to DNMT3B1; ΔDNMT3B1 and ΔDNMT3B2 contain a complete PWWP (proline-tryptophan-tryptophan-proline) motif while other variants either contained partial of the PWWP motif or completely lacked of the structure (FIG. 7B); ΔDNMT3B5-7 lack the enzymatic domains due to the alternative reading frames as a result of the alternative splicing (FIG. 7B).

To identify the individual ΔDNMT3B variants, specific PCR primer sets were designed on the basis of their splicing patterns (FIG. 8A). The ΔDNMT3B1 and ΔDNMT3B2 expression were detected in all 13 NSCLC cell lines analyzed, ΔDNMT3B4 expression in 12 of the 13 cell lines, and ΔDNMT3B6 expression in 7 of the 13 cell lines in contrast, ΔDNMT3B3, ΔDNMT3B5, and ΔDNMT3B7 were expressed infrequently (FIG. 8B). Interestingly, the DNMT3B variants were expressed less frequently and at lower levels in these cell lines (FIG. 8C). In a multiplex PCR analysis, the relative amplification efficiencies of the primer sets were determined for DNMT3B and ΔDNMT3B using DNA templates containing various concentrations of DNMT3B and ΔDNMT3B1 (FIG. 8D). The robust amplification of DNMT3B1 (FIG. 8D) indicated that the lack or very low levels of RT-PCR products in the cell lines reflected the low level of the corresponding transcripts.

Moreover, Table 3 illustrates characteristics and expression of ΔDNMT3B variants in primary NSCLC.

TABLE 3 Characterization and Expression of ΔDNMT3B Variants In Primary NSCLC Δ3B1 Δ3B2 Δ3B3 Δ3B4 Δ3B5 Δ3B6 Δ3B7 p16 RASSF Sex F 45 25 30 14 17 9 12 4 23 16 (56%) (67%) (31%) (38%) (20%) (27%) (9%) (51%) (36%) M 64 41 51 18 32 17 28 11 32 26 (64%) (80%) (28%) (50%) (27%) (44%) (17%) (50%) (41%) Smoke N 37 24 26 14 18 8 14 6 18 16 (65%) (70%) (38%) (49%) (22%) (38%) (16%) (49%) (43%) Y 72 42 55 18 31 18 26 9 37 26 (58%) (76%) (25%) (43%) (25%) (36%) (13%) (51%) (36%) Pathology Adeno 56 34 41 18 24 10 20 5 26 19 (61%) (73%) (32%) (43%) (18%) (36%) (9%) (46%) (34%) SCC 44 24 32 11 21 14 18 8 23 20 (55%) (73%) (25%) (48%) (32%) (41%) (18%) (52%) (46%) Differenti 5(50%) 6 4 4 0(0%) 1 0 6 2 Well 10 27 (60%) (40%) (40%) 8 (10%)* (0%)* (60%) (20%) Mod 42 (64%) 32 12 15 (19%) 13 6 21 16 Poor 34 (76%) (29%) (36%) 18 (31%) (14%) (50%) (38%) — — — — — — — — — — Stage I & II 70 43 55 21 34 17 25 8 33 28 (61%) (79%) (30%) (49%) (24%) (36%) (11%) (47%) (40%) III & IV 39 23 26 11 15 9 15 7 22 14 (59%) (67%) (28%) (39%) (23%) (39%) (18%) (56%) (36%)

Example 10 Expression of ΔDNMT3B4 Strongly Correlated with Promoter Methylation of Rassf1a iIn Primary NSCLC

In 109 primary NSCLC, the most frequently expressed variant was ΔDNMT3B2 (81 74%), followed by ΔDNMT3B1 (66 61%) and ΔDNMT3B4 (49 45%) (Table 4).

TABLE 4 Association Between Expression of ΔDNMT3B Variants and Promoter Methylation of P16 Or RASSF1A In Primary NSCLC Δ3B1 Δ3B2 Δ3B3 Δ3B4 Δ3B5 Δ3B6 Δ3B7 P16 Δ3B2 0  1 (3.6%) 1 65 (80.3%) p < 0.0001 Δ3B3 0 42 (54.6%) 53 (68.8%) 1 24 (75.0%) 28 (87.5%) p = 0.047 p = 0.03 Δ3B4 0 26 (43.3%) 35 (58.3%) 15 (25.0%) 1 40 (81.6%) 46 (93.9) 17 (34.7%) p < 0.0001 p < 0.0001 p < 0.27 Δ3B5 0 44 (53.0%) 55 (66.3%) 25 (30.1%) 26 (31.3%) 1 22 (84.6%) 26 (100%)  7 (26.9%) 23 (88.5%) p < 0.005 p < 0.0002 p < 0.75 p < 0.0001 Δ3B6 0 34 (49.3%) 41 (59.4%) 19 (27.5%) 20 (29.0%)  3 (4.4%) 1 32 (80.0%) 40 (100%) 13 (32.5%) 29 (72.5%) 23 (57.5%) p < 0.002 p < 0.0001 p < 0.58 p < 0.0001 p < 0.0001 Δ3B7 0 53 (56.4%) 67 (71.3%) 26 (27.7%) 38 (40.4%) 16 (17.0%) 27 (28.7%) 1 13 (86.7%) 14 (93.3%)  6 (40.0%) 11 (73.3%) 10 (66.7%) 13 (86.7%) p < 0.04 p < 0.06 p < 0.33 p < 0.02 p < 0.0002 p < 0.0001 P16 0 24 (44.4%) 33 (61.1%) 19 (35.2%) 19 (35.2%) 11 (20.4%) 16 (29.6%)  9 (16.7%) 1 42 (76.4%) 48 (87.3%) 13 (23.6%) 30 (54.6%) 15 (27.3%) 24 (43.6%)  6 (10.9%) p < 0.0007 p < 0.002 p < 0.19 p < 0.04 p < 0.40 p < 0.13 p < 0.38 RASSF1 0 32 (47.8%) 42 (62.7%) 21 (31.3%) 11 (16.4%)  6 (9.0%) 17 (25.4%)  4 (6.0%) 25 (37.3%) 1 34 (81.0%) 39 (92.9%) 11 (26.2%) 38 (90.5%) 20 (47.6%) 23 (54.8%) 11 (26.2%) 30 (71.4%) p < 0.0006 p < 0.0005 p < 0.57 p < 0.0001 p < 0.001 p < 0.002 p < 0.004 p < 0.0005

The expression of these variants was then correlated with the promoter methylation status of p16 and RASSF1A because these two genes are important in lung tumorigenesis and are frequently inactivated by promoter methylation in NSCLC (Burbee et al., 2001; Dammann et al., 2000; Merlo et al., 1995; Minna et al., 2002). There was a striking correlation between ΔDNMT3B4 expression and RASSF1A promoter methylation: 38 of the 42 (90%) tumors with RASSF1A promoter methylation expressed ΔDNMT3B4, whereas only 11 of the 67 (16%) tumors without RASSF1A promoter methylation expressed ΔDNMT3B4 (P<0.0001). The correlation between ΔDNMT3B4 and p16 promoter methylation, however, was not striking 30 of the 55 (55%) tumors with p16 promoter methylation expressed ΔDNMT3B4, and 19 of the 54 (35%) tumors without p16 promoter methylation expressed ΔDNMT3B4 (P=0.04). A multivariate analysis that included all the available variables showed that ΔDNMT3B7 expression, p16 promoter methylation, and ΔDNMT3B4 expression were independent factors associated with RASSF1A promoter methylation. Therefore, a logistic regression analysis was performed to adjust for ΔDNMT3B7 expression and p16 promoter methylation, and ΔDNMT3B4 still strongly correlated with RASSF1A promoter methylation (P<0.0001) after the adjustment. These data provided strong in vivo evidence that ΔDNMT3B4 is required for promoter methylation of RASSF1A in NSCLC.

Example 11 ΔDNMT3B4/2 Knockout Resulted in Rapid RASSF1A Promoter Demethylation and Reactivation of Gene Expression

A small interference RNA (siRNA) and an antisense RNA were designed to specifically target the junction of exon 5 and exon 7 of ΔDNMT3B. Because both ΔDNMT3B4 and ΔDNMT3B2 lack exon 6 (FIG. 8A), these molecules were expected to trigger degradation of both the ΔDNMT3B4 and the ΔDNMT3B2 transcripts. The NSCLC cell line H1299 was used for this study because it shows promoter methylation of both p16 and RASSF1A, lacks p16 and RASSF1A gene expression, and expresses a high level of ΔDNMT3B4 but not DNMT3B (FIGS. 8B and 8C, Table 5).

TABLE 5 Modification of DNA Methylation in Promoters and Repeat Sequences Method MSP MSP MSP MSP MSP MSP MSP Pyrosequencing Pyrosequencing Sequence name LINE methylation Alu methylation RIZ p14 MLH1 ECAD RASSF1A DAPK p16 (%) (%) H1299 control M M&U M 50.9 31.9 H1299 lipo M M&U M 54.9 28.4 H1299 siRNA U U M 35 23.6 H358 control M M 41.2 25.9 H358 lipo M M 40.3 26.4 H358 siRNA U M 39 25.3 RKO control M M M M M M 41 29.8 RKO lipo M M M M M M 46.4 30.8 RKO siRNA M M M M M M 44.6 30.5 SW48 control M M M&U M M 56.3 30.1 SW48 lipo M M M&U M M 61.8 32.6 M: methylated promoter; U: unmethylated promoter; M&U: mixed with both methylated and unmethylated promoters; control: treated with medium alone; lipo: treated with lipofectamine alone; siRNA: treated with ΔDNMT3B4/2-specific siRNA

The siRNA or the antisense RNA successfully eliminated transcripts of ΔDNMT3B2 and ΔDNMT3B4 in H1299 cells in a dose- and time-dependent manner but had no effect on ΔDNMT3B1 (FIG. 9A). The effect was specific because the expression levels of the three transcripts in cells treated with medium, lipofectamine alone, lipofectamine plus scramble siRNA, or lipofectamine plus siRNA-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) did not change (FIG. 9A).

The effect of a ΔDNMT3B4/2 knockout was analyzed in the promoter methylation of p16 and RASSF1A. The RASSF1A promoter became partially unmethylated in the cells treated with 20 nM siRNA-ΔDNMT3B4/2 and completely unmethylated (defined as substantially no detectable methylated PCR product in by methylation-specific PCR studies) in cells treated with 40 nM siRNA at 12 h (FIG. 9B). At 24 h, the promoter was completely unmethylated in the cells treated with 20 nM siRNA or 40 nM antisense RNA, whereas it was completely demethylated at 48 h in the cells treated with 10 nM siRNA (FIG. 9B). These results were consistent with the dose-dependent reduction of ΔDNMT3B4 expression resulting from the siRNA or antisense RNA treatment (FIG. 9A). In contrast, promoter methylation of p16 was not affected by the treatment (FIG. 9B). Interestingly, RASSF1A remained completely unmethylated 72 h after the short-term siRNA or antisense RNA treatment (FIG. 9B).

The expression status of RASSF1A was analyzed using RT-PCR. Expression of RASSF1A was restored in cells treated with 40 nM siRNA-ΔDNMT3B4/2 or 40 nM antisense RNA at 12 h, with 20 nM siRNA at 24 h, and with 10 nM siRNA at 48 h (FIG. 9C). RASSF1A expression was restored for at least 72 h after treatment (FIG. 9C). The result was again consistent with the dose-dependent reduction of ΔDNMT3B4 resulting from the siRNA or antisense treatment (FIG. 9A).

Next, bisulfite sequencing of methylation-specific PCR products from cells treated with or without siRNA-ΔDNMT3B4/2 was performed. The fragment sequenced was part of the RASSF1A promoter and contained 10 CpG sites in addition to those in the primer sequences. The cytosine residuals at these 10 CpG sites were not converted to uracil (recognized as thymidine in PCR products) by the bisulfite (an indication of methylation) in any of the 14 clones derived from the cells 12 h after treatment with 40 nM siRNA-GAPDH, whereas the cytosine residuals at all 10 CpG sites were converted to uracil by the bisulfite (an indication of unmethylated status), in all 14 clones derived from the cells 12 h after treatment with 40 nM siRNA-ΔDNMT3B4/2 (FIG. 9D). This difference indicated that the siRNA treatment had completely reversed the methylated CpG sites in the RASSF1A promoter region.

To exclude the possibility that the treatment might affect DNMT1, the major enzyme responsible for maintaining DNA methylation, DNMT1 protein expression was analyzed in H1299 cells treated with siRNA and found no reduction in protein level (FIG. 9E), suggesting that DNMT1 was not the contributing factor to the observed promoter demethylation.

H358 cells were also analyzed, another NSCLC cell line with p16 and RASSF1A promoter methylation and ΔDNMT3B4/2 expression (FIG. 8B). As with H1299, the treatment knocked out ΔDNMT3B4/2 expression and resulted in the demethylation of the RASSF1A promoter but not of the p16 promoter (Table 5).

Example 12 ΔDNMT3B4/2 Knockout Suppressed Cell Growth and Increased Cell Death in NSCLC Cells

A microelectronic cell sensor system was used (ACEA Biosciences, Inc., San Diego, Calif.) to determine the dynamic change in cell growth affected by the ΔDNMT3B4/2 knockout (measured every 30 min). In the H1299 cells, growth was inhibited at about 10 h after treatment with the siRNA-ΔDNMT3B4/2 in a dose-dependent manner or the antisense RNA (FIG. 10A). To determine the potential mechanism for inhibiting the growth of the ΔDNMT3B4/2 knockout, the cell cycle distribution of the H1299 cells was examined 24 h after treatment using flow cytometry. There was a dose-dependent increase of the sub-G1 fraction in the cells treated with the siRNA-ΔDNMT3B4/2 or the antisense RNA (FIG. 10B). This increase indicated that the treatment had induced cell death.

Example 13 ΔDNMT3B4/2 Knockout had Various Effects on Other CpG Sequences and in Colorectal Cancer Cells

By screening other promoters commonly methylated in lung cancers, a 50% methylated death-associated protein (DAP)-kinase promoter in the H1299 cells was identified; such methylation was completely eliminated after the siRNA-ΔDNMT3B4/2 treatment (Table 5). Then, using pyrosequencing, we analyzed the effect of the siRNA-ΔDNMT3B4/2 in repeat DNA sequences (Alu and LINE). This analysis indicated a more global DNA methylation status (Yang et al., 2004). In the H1299 cells, the treatment resulted in reduced DNA methylation in the LINE and Alu sequences but not in the H358 cells (Table 5). Two colorectal cancer cell lines (SW48 and RKO) were analyzed to determine whether the effect of the siRNA-ΔDNMT3B4/2 observed in the NSCLC cell lines also occurred in other tumor types. DNA methylation occurred in these cell lines in more promoters (Table 5), and numerous ΔDNMT3B4/2 transcripts were expressed (data not shown). Interestingly, none of these promoters, including RASSF1A, or the repeat sequences were demethylated after ΔDNMT3B4/2 was knocked out by the siRNA-ΔDNMT3B4/2 (Table 5).

Example 14 Rare ΔDNMT3B Variants and Clinical Outcome

FIG. 11 illustrates expression of rare ΔDNMT3B variants, particularly ΔDNMT3B5, ΔDNMT3B6, and ΔDNMT3B7, and the clinical outcome in patients with NSCLC. For FIG. 11. deltaDNMT3B5-7 (E-G) were less frequently expressed in NSCLC and never detected in normal lung tissues by using PCR primers specific to these isoforms. However, patients whose tumors expressed these rare deltaDNMT3B isoforms showed statistically significant poorer outcome (both overall survival and disease-specific survival) compared to those patients whose tumors had no expression of these rare isoforms. Thus, in specific embodiments, the presence of these isoforms indicates a poor prognosis (decreased survival/lifespan) in patients compared to patients which lack these isoforms.

Furthermore, FIG. 12 demonstrates expression of the ΔDNMT3B4 variant from bronchial brush cells.

Expression of deltaDNMT3B isoforms was analyzed using PCR primers specific to each isoform in 87 bronchial brush specimens obtained from chronic smokers without clinical evidence of lung cancer. We found expression of deltaDNMT3B1 in 30% of the samples, deltaDNMT3B2 in 79% of the samples, and deltaDNMT3B4 in only 1% of the sample, suggesting deltaDNMT3B1/2 are activated in very early stage lung carcinogenesis following long term smoking while activation of deltaDNMT3B4 is a relatively late event. These data are consistent with frequent identification of p16 promoter methylation in such tissues while RASSF1A promoter methylation is rarely identified in these samples. In FIG. 12, however, examples of deltaDNMT3B4 expression in the bronchial brush samples is provided. The only positive sample was shown in the figure. In specific embodiments of the invention, this indicates that the appearance of this variant occurs in later stages of cancer and may be diagnostic thereof.

Example 15 Antibodies for ΔDNMT3B Variants

Antibodies directed to the ΔDNMT3B variants may be generated by standard means in the art. In specific aspects of the invention, the antibodies are monoclonal, although in alternative embodiments the antibodies are polyclonal.

Monoclonal antibodies may be generated, for example, in mice and recognize specific peptides used to generate these antibodies, as well as recombinant isoforms of DNMT3Bs. Antibodies produced in all clones described below are IgG.

Clones 185A1 and 185A2 are generated against peptide sequence: ESPQVEADSGD (SEQ ID NO:66), which is shared by most of the delta isoforms as well as DNMT3Bs. IgG clone 187B1 is generated against peptide sequence: GLKPNNTQP-ENKTRC (SEQ ID NO:67), which contains the junction specific for delta-DNMT3B2/4. All the clones have been confirmed to recognize specific delta-DNMT3B4 recombinant protein generated in E coli. FIG. 13 shows proteins recognized by the antibodies in lysate of H460 NSCLC cell line.

In particular aspects of the invention, antibodies are utilized to bind to the corresponding variant(s), thereby providing a therapeutic composition for cancer treatment, such as treatment of NSCLC. That is, antibodies for the variants are generated or provided otherwise, such as through commercial means, and administered to a patient in need thereof, such as a cancer patient. In particular embodiments, the antibodies are administered in addition to another cancer therapy, such as one provided prior to, concomitant with, and/or subsequent to the antibody administration. Additional cancer therapies include chemotherapy, radiation, surgery, gene therapy, immunotherapy hormone therapy, and so forth.

All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

REFERENCES

The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.

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1. An isolated nucleic acid sequence encoding a DNA methyltransferase-3B variant having the amino acid sequence selected from the group consisting of SEQ ID NO:16, SEQ ID NO:17, and SEQ ID NO:18.
 2. The nucleic acid sequence of claim 1, comprising a DNA methyltransferase-3B variant nucleic acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:4.
 3. The isolated nucleic acid of claim 2, wherein the nucleic acid sequence is comprised in an expression vector.
 4. The isolated nucleic acid of claim 3, wherein the expression vector is further defined as a viral or plasmid vector.
 5. The isolated nucleic acid of claim 4, wherein the viral vector is an adenoviral vector, an adeno-associated viral vector, a retroviral vector, a lentiviral vector, a herpes viral vector, polyoma viral vector or hepatitis B viral vector.
 6. The isolated nucleic acid sequence of claim 3, wherein the expression vector is comprised in a non-viral delivery system.
 7. The isolated nucleic acid sequence of claim 6, wherein the non-viral delivery system comprises one or more lipids.
 8. The isolated nucleic acid sequence of claim 2, wherein the nucleic acid sequence is operatively linked to a promoter.
 9. A host cell comprising a nucleic acid sequence encoding a DNA methyltransferase-3B variant according to claim
 2. 10. The host cell of claim 9, wherein the nucleic acid sequence is comprised in a vector.
 11. An isolated DNA methyltransferase-3B variant having the amino acid sequence selected from the group consisting of SEQ ID NO:16, SEQ ID NO:17, and SEQ ID NO:18.
 12. The nucleic acid sequence of claim 2, wherein said sequence is SEQ ID NO:2.
 13. The nucleic acid sequence of claim 2, wherein said sequence is SEQ ID NO:3.
 14. The nucleic acid sequence of claim 2, wherein said sequence is SEQ ID NO:4.
 15. The nucleic acid sequence of claim 1, encoding a DNA methyltransferase-3B variant having the amino acid sequence of SEQ ID NO:16.
 16. The nucleic acid sequence of claim 1, encoding a DNA methyltransferase-3B variant having the amino acid sequence of SEQ ID NO:17.
 17. The nucleic acid sequence of claim 1, encoding a DNA methyltransferase-3B variant having the amino acid sequence of SEQ ID NO:18.
 18. The DNA methyltransferase-3B variant of claim 11, having the amino acid sequence of SEQ ID NO:16.
 19. The DNA methyltransferase-3B variant of claim 11, having the amino acid sequence of SEQ ID NO:17.
 20. The DNA methyltransferase-3B variant of claim 11, having the amino acid sequence of SEQ ID NO:18. 